From 8809fcfffd740499d0f03102c28d406c2cd31b93 Mon Sep 17 00:00:00 2001
From: Thomas Schmelzer <thomas.schmelzer@gmail.com>
Date: Thu, 16 Apr 2026 06:49:03 +0400
Subject: [PATCH 1/5] chore: prepare rhiza sync infrastructure

Update rhiza tooling to use sync command (replacing deprecated materialize),
bump .rhiza-version to 0.12.1, and add bootstrap.mk with install-uv target.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .rhiza/.rhiza-version      |   2 +-
 .rhiza/make.d/bootstrap.mk | 107 +++++++++++++++++++++
 .rhiza/rhiza.mk            | 189 ++++++-------------------------------
 .rhiza/template.yml        |  37 ++++----
 4 files changed, 154 insertions(+), 181 deletions(-)
 create mode 100644 .rhiza/make.d/bootstrap.mk

diff --git a/.rhiza/.rhiza-version b/.rhiza/.rhiza-version
index 899f24fc..34a83616 100644
--- a/.rhiza/.rhiza-version
+++ b/.rhiza/.rhiza-version
@@ -1 +1 @@
-0.9.0
\ No newline at end of file
+0.12.1
diff --git a/.rhiza/make.d/bootstrap.mk b/.rhiza/make.d/bootstrap.mk
new file mode 100644
index 00000000..374c433a
--- /dev/null
+++ b/.rhiza/make.d/bootstrap.mk
@@ -0,0 +1,107 @@
+## .rhiza/make.d/bootstrap.mk - Bootstrap and Installation
+# This file provides targets for setting up the development environment,
+# installing dependencies, and cleaning project artifacts.
+
+# Declare phony targets (they don't produce files)
+.PHONY: install-uv install clean pre-install post-install
+
+# Hook targets (double-colon rules allow multiple definitions)
+pre-install:: ; @:
+post-install:: ; @:
+
+##@ Bootstrap
+install-uv: ## ensure uv/uvx is installed
+	# Ensure the ${INSTALL_DIR} folder exists
+	@mkdir -p ${INSTALL_DIR}
+
+	# Install uv/uvx only if they are not already present in PATH or in the install dir
+	@if command -v uv >/dev/null 2>&1 && command -v uvx >/dev/null 2>&1; then \
+	  :; \
+	elif [ -x "${INSTALL_DIR}/uv" ] && [ -x "${INSTALL_DIR}/uvx" ]; then \
+	  printf "${BLUE}[INFO] uv and uvx already installed in ${INSTALL_DIR}, skipping.${RESET}\n"; \
+	else \
+	  printf "${BLUE}[INFO] Installing uv and uvx into ${INSTALL_DIR}...${RESET}\n"; \
+	  if ! curl -LsSf https://astral.sh/uv/install.sh | UV_INSTALL_DIR="${INSTALL_DIR}" sh >/dev/null 2>&1; then \
+	    printf "${RED}[ERROR] Failed to install uv${RESET}\n"; \
+	    exit 1; \
+	  fi; \
+	fi
+
+install: pre-install install-uv ## install
+	# Create the virtual environment only if it doesn't exist
+	@if [ ! -d "${VENV}" ]; then \
+	  ${UV_BIN} venv $(if $(PYTHON_VERSION),--python $(PYTHON_VERSION)) ${VENV} || { printf "${RED}[ERROR] Failed to create virtual environment${RESET}\n"; exit 1; }; \
+	else \
+	  printf "${BLUE}[INFO] Using existing virtual environment at ${VENV}, skipping creation${RESET}\n"; \
+	fi
+
+	# Install the dependencies from pyproject.toml (if it exists)
+	@if [ -f "pyproject.toml" ]; then \
+	  if [ -f "uv.lock" ]; then \
+	    if ! ${UV_BIN} lock --check >/dev/null 2>&1; then \
+	      printf "${YELLOW}[WARN] uv.lock is out of sync with pyproject.toml${RESET}\n"; \
+	      printf "${YELLOW}       Run 'uv sync' to update your lock file and environment${RESET}\n"; \
+	      printf "${YELLOW}       Or run 'uv lock' to update only the lock file${RESET}\n"; \
+	      exit 1; \
+	    fi; \
+	    printf "${BLUE}[INFO] Installing dependencies from lock file${RESET}\n"; \
+	    ${UV_BIN} sync --all-extras --all-groups --frozen || { printf "${RED}[ERROR] Failed to install dependencies${RESET}\n"; exit 1; }; \
+	  else \
+	    printf "${YELLOW}[WARN] uv.lock not found. Generating lock file and installing dependencies...${RESET}\n"; \
+	    ${UV_BIN} sync --all-extras || { printf "${RED}[ERROR] Failed to install dependencies${RESET}\n"; exit 1; }; \
+	  fi; \
+	else \
+	  printf "${YELLOW}[WARN] No pyproject.toml found, skipping install${RESET}\n"; \
+	fi
+
+	# Install dev dependencies from .rhiza/requirements/*.txt files
+	@if [ -d ".rhiza/requirements" ] && ls .rhiza/requirements/*.txt >/dev/null 2>&1; then \
+	  for req_file in .rhiza/requirements/*.txt; do \
+	    if [ -f "$$req_file" ]; then \
+	      printf "${BLUE}[INFO] Installing requirements from $$req_file${RESET}\n"; \
+	      ${UV_BIN} pip install -r "$$req_file" || { printf "${RED}[ERROR] Failed to install requirements from $$req_file${RESET}\n"; exit 1; }; \
+	    fi; \
+	  done; \
+	fi
+
+	# Check if there is requirements.txt file in the tests folder (legacy support)
+	@if [ -f "tests/requirements.txt" ]; then \
+	  printf "${BLUE}[INFO] Installing requirements from tests/requirements.txt${RESET}\n"; \
+	  ${UV_BIN} pip install -r tests/requirements.txt || { printf "${RED}[ERROR] Failed to install test requirements${RESET}\n"; exit 1; }; \
+	fi
+
+	# Install pre-commit hooks
+	@if [ -f ".pre-commit-config.yaml" ]; then \
+	  printf "${BLUE}[INFO] Installing pre-commit hooks...${RESET}\n"; \
+	  ${UVX_BIN} -p ${PYTHON_VERSION} pre-commit install || { printf "${YELLOW}[WARN] Failed to install pre-commit hooks${RESET}\n"; }; \
+	fi
+
+	@$(MAKE) post-install
+	
+	# Display success message with activation instructions
+	@printf "\n${GREEN}[SUCCESS] Installation complete!${RESET}\n\n"
+	@printf "${BLUE}To activate the virtual environment, run:${RESET}\n"
+	@printf "${YELLOW}  source ${VENV}/bin/activate${RESET}\n\n"
+
+clean: ## Clean project artifacts and stale local branches
+	@printf "%bCleaning project...%b\n" "$(BLUE)" "$(RESET)"
+
+	# Remove ignored files/directories, but keep .env files, tested with futures project
+	@git clean -d -X -f \
+		-e '!.env' \
+		-e '!.env.*'
+
+	# Remove build & test artifacts
+	@rm -rf \
+		dist \
+		build \
+		*.egg-info \
+		.coverage \
+		.pytest_cache \
+		.benchmarks
+
+	@printf "%bRemoving local branches with no remote counterpart...%b\n" "$(BLUE)" "$(RESET)"
+
+	@git fetch --prune
+
+	@git branch -vv | awk '/: gone]/{print $$1}' | xargs -r git branch -D
diff --git a/.rhiza/rhiza.mk b/.rhiza/rhiza.mk
index a03538b3..25282eaf 100644
--- a/.rhiza/rhiza.mk
+++ b/.rhiza/rhiza.mk
@@ -1,7 +1,7 @@
 ## Makefile for jebel-quant/rhiza
 # (https://github.com/jebel-quant/rhiza)
 #
-# Purpose: Developer tasks using uv/uvx (install, test, docs, marimushka, book).
+# Purpose: Developer tasks using uv/uvx (install, test, book).
 # Lines with `##` after a target are parsed into help text,
 # and lines starting with `##@` create section headers in the help output.
 #
@@ -18,14 +18,7 @@ RESET := \033[0m
 
 # Declare phony targets (they don't produce files)
 .PHONY: \
-	bump \
-	clean \
-	deptry \
-	fmt \
-	mypy \
 	help \
-	install \
-	install-uv \
 	post-bump \
 	post-install \
 	post-release \
@@ -36,10 +29,10 @@ RESET := \033[0m
 	pre-release \
 	pre-sync \
 	pre-validate \
-	release \
-	sync \
+	print-logo \
+	readme \
 	summarise-sync \
-	update-readme \
+	sync \
 	validate \
 	version-matrix
 
@@ -54,29 +47,21 @@ PYTHON_VERSION ?= $(shell cat .python-version 2>/dev/null || echo "3.13")
 export PYTHON_VERSION
 
 # Read Rhiza version from .rhiza/.rhiza-version (single source of truth for rhiza-tools)
-RHIZA_VERSION ?= $(shell cat .rhiza/.rhiza-version 2>/dev/null || echo "0.9.0")
+RHIZA_VERSION ?= $(shell cat .rhiza/.rhiza-version 2>/dev/null || echo "0.10.2")
 export RHIZA_VERSION
 
 export UV_NO_MODIFY_PATH := 1
 export UV_VENV_CLEAR := 1
 
+# Unset VIRTUAL_ENV to prevent uv from warning about path mismatches
+# when a virtual environment is already activated in the shell
+unexport VIRTUAL_ENV
+
 # Load .rhiza/.env (if present) and export its variables so recipes see them.
 -include .rhiza/.env
 
-# Include split Makefiles
--include tests/tests.mk
--include book/book.mk
--include book/marimo/marimo.mk
--include presentation/presentation.mk
--include docker/docker.mk
--include .github/agents/agentic.mk
-# .rhiza/rhiza.mk is INLINED below
--include .github/github.mk
-
-
-
 # ==============================================================================
-# Rhiza Core Actions (formerly .rhiza/rhiza.mk)
+# Rhiza Core
 # ==============================================================================
 
 # RHIZA_LOGO definition
@@ -91,19 +76,15 @@ endef
 export RHIZA_LOGO
 
 # Declare phony targets for Rhiza Core
-.PHONY: print-logo sync validate readme pre-sync post-sync pre-validate post-validate
+.PHONY: print-logo sync sync-experimental materialize validate readme pre-sync post-sync pre-validate post-validate
 
 # Hook targets (double-colon rules allow multiple definitions)
+# Note: pre-install/post-install are defined in bootstrap.mk
+# Note: pre-bump/post-bump/pre-release/post-release are defined in releasing.mk
 pre-sync:: ; @:
 post-sync:: ; @:
 pre-validate:: ; @:
 post-validate:: ; @:
-pre-install:: ; @:
-post-install:: ; @:
-pre-release:: ; @:
-post-release:: ; @:
-pre-bump:: ; @:
-post-bump:: ; @:
 
 ##@ Rhiza Workflows
 
@@ -116,152 +97,42 @@ sync: pre-sync ## sync with template repository as defined in .rhiza/template.ym
 		printf "${BLUE}[INFO] Skipping sync in rhiza repository (no template.yml by design)${RESET}\n"; \
 	else \
 		$(MAKE) install-uv; \
-		${UVX_BIN} "rhiza>=$(RHIZA_VERSION)" materialize --force .; \
+		${UVX_BIN} "rhiza==$(RHIZA_VERSION)" sync .; \
 	fi
 	@$(MAKE) post-sync
 
+materialize: ## [DEPRECATED] use 'make sync' instead — materialize --force is now sync
+	@printf "${YELLOW}[WARN] 'make materialize' is deprecated and will be removed in a future release.${RESET}\n"
+	@printf "${YELLOW}[WARN] Please use 'make sync' instead (e.g. 'materialize --force' is now 'make sync').${RESET}\n"
+	@$(MAKE) sync
+
 summarise-sync: install-uv ## summarise differences created by sync with template repository
 	@if git remote get-url origin 2>/dev/null | grep -iqE 'jebel-quant/rhiza(\.git)?$$'; then \
 		printf "${BLUE}[INFO] Skipping summarise-sync in rhiza repository (no template.yml by design)${RESET}\n"; \
 	else \
 		$(MAKE) install-uv; \
-		${UVX_BIN} "rhiza>=$(RHIZA_VERSION)" summarise .; \
+		${UVX_BIN} "rhiza==$(RHIZA_VERSION)" summarise .; \
+	fi
+
+rhiza-test: install ## run rhiza's own tests (if any)
+	@if [ -d ".rhiza/tests" ]; then \
+		${UV_BIN} run pytest .rhiza/tests; \
+	else \
+		printf "${YELLOW}[WARN] No .rhiza/tests directory found, skipping rhiza-tests${RESET}\n"; \
 	fi
 
-validate: pre-validate ## validate project structure against template repository as defined in .rhiza/template.yml
+validate: pre-validate rhiza-test ## validate project structure against template repository as defined in .rhiza/template.yml
 	@if git remote get-url origin 2>/dev/null | grep -iqE 'jebel-quant/rhiza(\.git)?$$'; then \
 		printf "${BLUE}[INFO] Skipping validate in rhiza repository (no template.yml by design)${RESET}\n"; \
 	else \
 		$(MAKE) install-uv; \
-		${UVX_BIN} "rhiza>=$(RHIZA_VERSION)" validate .; \
+		${UVX_BIN} "rhiza==$(RHIZA_VERSION)" validate .; \
 	fi
 	@$(MAKE) post-validate
 
 readme: install-uv ## update README.md with current Makefile help output
 	@${UVX_BIN} "rhiza-tools>=0.2.0" update-readme
 
-# ==============================================================================
-# End Rhiza Core Actions
-# ==============================================================================
-
-##@ Bootstrap
-install-uv: ## ensure uv/uvx is installed
-	# Ensure the ${INSTALL_DIR} folder exists
-	@mkdir -p ${INSTALL_DIR}
-
-	# Install uv/uvx only if they are not already present in PATH or in the install dir
-	@if command -v uv >/dev/null 2>&1 && command -v uvx >/dev/null 2>&1; then \
-	  :; \
-	elif [ -x "${INSTALL_DIR}/uv" ] && [ -x "${INSTALL_DIR}/uvx" ]; then \
-	  printf "${BLUE}[INFO] uv and uvx already installed in ${INSTALL_DIR}, skipping.${RESET}\n"; \
-	else \
-	  printf "${BLUE}[INFO] Installing uv and uvx into ${INSTALL_DIR}...${RESET}\n"; \
-	  if ! curl -LsSf https://astral.sh/uv/install.sh | UV_INSTALL_DIR="${INSTALL_DIR}" sh >/dev/null 2>&1; then \
-	    printf "${RED}[ERROR] Failed to install uv${RESET}\n"; \
-	    exit 1; \
-	  fi; \
-	fi
-
-install: pre-install install-uv ## install
-	# Create the virtual environment only if it doesn't exist
-	@if [ ! -d "${VENV}" ]; then \
-	  ${UV_BIN} venv $(if $(PYTHON_VERSION),--python $(PYTHON_VERSION)) ${VENV} || { printf "${RED}[ERROR] Failed to create virtual environment${RESET}\n"; exit 1; }; \
-	else \
-	  printf "${BLUE}[INFO] Using existing virtual environment at ${VENV}, skipping creation${RESET}\n"; \
-	fi
-
-	# Install the dependencies from pyproject.toml (if it exists)
-	@if [ -f "pyproject.toml" ]; then \
-	  if [ -f "uv.lock" ]; then \
-	    printf "${BLUE}[INFO] Installing dependencies from lock file${RESET}\n"; \
-	    ${UV_BIN} sync --all-extras --all-groups --frozen || { printf "${RED}[ERROR] Failed to install dependencies${RESET}\n"; exit 1; }; \
-	  else \
-	    printf "${YELLOW}[WARN] uv.lock not found. Generating lock file and installing dependencies...${RESET}\n"; \
-	    ${UV_BIN} sync --all-extras || { printf "${RED}[ERROR] Failed to install dependencies${RESET}\n"; exit 1; }; \
-	  fi; \
-	else \
-	  printf "${YELLOW}[WARN] No pyproject.toml found, skipping install${RESET}\n"; \
-	fi
-
-	# Install dev dependencies from .rhiza/requirements/*.txt files
-	@if [ -d ".rhiza/requirements" ] && ls .rhiza/requirements/*.txt >/dev/null 2>&1; then \
-	  for req_file in .rhiza/requirements/*.txt; do \
-	    if [ -f "$$req_file" ]; then \
-	      printf "${BLUE}[INFO] Installing requirements from $$req_file${RESET}\n"; \
-	      ${UV_BIN} pip install -r "$$req_file" || { printf "${RED}[ERROR] Failed to install requirements from $$req_file${RESET}\n"; exit 1; }; \
-	    fi; \
-	  done; \
-	fi
-
-	# Check if there is requirements.txt file in the tests folder (legacy support)
-	@if [ -f "tests/requirements.txt" ]; then \
-	  printf "${BLUE}[INFO] Installing requirements from tests/requirements.txt${RESET}\n"; \
-	  ${UV_BIN} pip install -r tests/requirements.txt || { printf "${RED}[ERROR] Failed to install test requirements${RESET}\n"; exit 1; }; \
-	fi
-	@$(MAKE) post-install
-
-clean: ## Clean project artifacts and stale local branches
-	@printf "%bCleaning project...%b\n" "$(BLUE)" "$(RESET)"
-
-	# Remove ignored files/directories, but keep .env files, tested with futures project
-	@git clean -d -X -f \
-		-e '!.env' \
-		-e '!.env.*'
-
-	# Remove build & test artifacts
-	@rm -rf \
-		dist \
-		build \
-		*.egg-info \
-		.coverage \
-		.pytest_cache \
-		.benchmarks
-
-	@printf "%bRemoving local branches with no remote counterpart...%b\n" "$(BLUE)" "$(RESET)"
-
-	@git fetch --prune
-
-	@git branch -vv | awk '/: gone]/{print $$1}' | xargs -r git branch -D
-
-##@ Quality and Formatting
-deptry: install-uv ## Run deptry
-	@if [ -d ${SOURCE_FOLDER} ]; then \
-		$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${SOURCE_FOLDER}; \
-	fi
-
-	@if [ -d ${MARIMO_FOLDER} ]; then \
-		if [ -d ${SOURCE_FOLDER} ]; then \
-			$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${MARIMO_FOLDER} ${SOURCE_FOLDER} --ignore DEP004; \
-		else \
-		  	$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${MARIMO_FOLDER} --ignore DEP004; \
-		fi \
-	fi
-
-fmt: install-uv ## check the pre-commit hooks and the linting
-	@${UVX_BIN} -p ${PYTHON_VERSION} pre-commit run --all-files
-
-mypy: install-uv ## run mypy analysis
-	@if [ -d ${SOURCE_FOLDER} ]; then \
-		${UVX_BIN} -p ${PYTHON_VERSION} mypy ${SOURCE_FOLDER} --strict --config-file=pyproject.toml; \
-	fi
-
-##@ Releasing and Versioning
-bump: pre-bump ## bump version
-	@if [ -f "pyproject.toml" ]; then \
-		$(MAKE) install; \
-		${UVX_BIN} "rhiza[tools]>=0.8.6" tools bump; \
-		printf "${BLUE}[INFO] Updating uv.lock file...${RESET}\n"; \
-		${UV_BIN} lock; \
-	else \
-		printf "${YELLOW}[WARN] No pyproject.toml found, skipping bump${RESET}\n"; \
-	fi
-	@$(MAKE) post-bump
-
-release: pre-release install-uv ## create tag and push to remote with prompts
-	@UV_BIN="${UV_BIN}" /bin/sh ".rhiza/scripts/release.sh"
-	@$(MAKE) post-release
-
-
 ##@ Meta
 
 help: print-logo ## Display this help message
@@ -272,7 +143,7 @@ help: print-logo ## Display this help message
 	+@printf "\n"
 
 version-matrix: install-uv ## Emit the list of supported Python versions from pyproject.toml
-	@${UV_BIN} run .rhiza/utils/version_matrix.py
+	@${UVX_BIN} "rhiza-tools>=0.2.2" version-matrix
 
 print-% : ## print the value of a variable (usage: make print-VARIABLE)
 	@printf "${BLUE}[INFO] Printing value of variable '$*':${RESET}\n"
diff --git a/.rhiza/template.yml b/.rhiza/template.yml
index 1fb7976d..6a7d0141 100644
--- a/.rhiza/template.yml
+++ b/.rhiza/template.yml
@@ -1,22 +1,17 @@
-template-repository: jebel-quant/rhiza
-template-branch: main
-include:
-- .github/workflows
-- .editorconfig
-- .gitignore
-- .pre-commit-config.yaml
-- CODE_OF_CONDUCT.md
-- CONTRIBUTING.md
-- Makefile
-- ruff.toml
-- .rhiza
-- book
-- renovate.json
-exclude:
-- .github/workflows/rhiza_docker.yml
-- .github/workflows/rhiza_devcontainer.yml
-- .github/workflows/rhiza_ci.yml
-- .github/workflows/rhiza_security.yml
-- .github/dependabot.yml
-- .rhiza/docs
+template-repository: "jebel-quant/rhiza"
+template-branch: "v0.9.5"
+
+templates:
+  - github
+  - marimo
 
+exclude:
+  - .rhiza/docs/
+  - .rhiza/make.d/agentic.mk
+  - .rhiza/make.d/gh-aw.mk
+  - .rhiza/make.d/github.mk
+  - .rhiza/make.d/custom-env.mk
+  - .rhiza/make.d/custom-task.mk
+  - .rhiza/make.d/README.md
+  - .github/agents/
+  - docs/adr

From 2f7b64063a2017cab7e166b8e3238ed011e5f655 Mon Sep 17 00:00:00 2001
From: Thomas Schmelzer <thomas.schmelzer@gmail.com>
Date: Thu, 16 Apr 2026 06:50:06 +0400
Subject: [PATCH 2/5] chore: sync with rhiza template v0.9.5

Applied rhiza template sync from jebel-quant/rhiza@v0.9.5. Added new
GitHub templates, workflows, hooks, and make.d files; removed deprecated
workflows and orphaned files.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/DISCUSSION_TEMPLATE/q-and-a.yml       |  25 +
 .github/ISSUE_TEMPLATE/bug_report.yml         |  57 ++
 .github/ISSUE_TEMPLATE/feature_request.yml    |  41 ++
 .github/actions/configure-git-auth/README.md  |  80 +++
 .github/actions/configure-git-auth/action.yml |  21 +
 .github/copilot-instructions.md               | 181 +++++
 .github/dependabot.yml                        |  80 +++
 .github/hooks/hooks.json                      |  21 +
 .github/hooks/session-end.sh                  |  36 +
 .github/hooks/session-start.sh                |  37 ++
 .github/secret_scanning.yml                   |  20 +
 .github/semgrep.yml                           |  84 +++
 .github/workflows/copilot-setup-steps.yml     |  50 ++
 .github/workflows/rhiza_book.yml              |  33 +-
 .github/workflows/rhiza_codeql.yml            | 125 ----
 .github/workflows/rhiza_deptry.yml            |  40 --
 .github/workflows/rhiza_marimo.yml            |  32 +-
 .github/workflows/rhiza_mypy.yml              |  34 -
 .github/workflows/rhiza_pre-commit.yml        |  37 --
 .github/workflows/rhiza_release.yml           | 173 +++--
 .github/workflows/rhiza_sync.yml              | 114 +++-
 .github/workflows/rhiza_validate.yml          |  27 -
 .github/workflows/rhiza_weekly.yml            | 118 ++++
 .gitignore                                    |  24 +
 .pre-commit-config.yaml                       |  41 +-
 .python-version                               |   1 +
 .rhiza/.cfg.toml                              |  12 +-
 .rhiza/.env                                   |  13 +-
 .rhiza/assets/rhiza-logo.svg                  |  81 +++
 .rhiza/make.d/01-custom-env.mk                |   9 -
 .rhiza/make.d/10-custom-task.mk               |  12 -
 .rhiza/make.d/book.mk                         |  99 +++
 .rhiza/make.d/marimo.mk                       |  42 ++
 .rhiza/make.d/quality.mk                      |  51 ++
 .rhiza/make.d/releasing.mk                    |  50 ++
 .rhiza/requirements/README.md                 |   6 +-
 .rhiza/requirements/docs.txt                  |   4 +-
 .rhiza/requirements/tests.txt                 |  12 -
 .rhiza/requirements/tools.txt                 |   3 +-
 .rhiza/scripts/check_workflow_names.py        |  73 --
 .rhiza/scripts/release.sh                     | 276 --------
 .rhiza/template.lock                          |  64 ++
 .rhiza/utils/version_matrix.py                | 152 -----
 CODE_OF_CONDUCT.md                            |  27 -
 CONTRIBUTING.md                               |  93 ---
 Makefile                                      |  41 ++
 book/README.md                                |  67 --
 book/book.mk                                  | 166 -----
 book/marimo/marimo.mk                         |  67 --
 book/marimo/notebooks/rhiza.py                | 629 ------------------
 book/minibook-templates/custom.html.jinja2    | 210 ------
 docs/assets/rhiza-logo.svg                    |  81 +++
 .../README.md => docs/development/MARIMO.md   |  10 +-
 docs/index.md                                 |   2 +
 docs/mkdocs-base.yml                          |  71 ++
 renovate.json                                 |  29 -
 ruff.toml                                     |  40 +-
 57 files changed, 1798 insertions(+), 2226 deletions(-)
 create mode 100644 .github/DISCUSSION_TEMPLATE/q-and-a.yml
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml
 create mode 100644 .github/actions/configure-git-auth/README.md
 create mode 100644 .github/actions/configure-git-auth/action.yml
 create mode 100644 .github/copilot-instructions.md
 create mode 100644 .github/dependabot.yml
 create mode 100644 .github/hooks/hooks.json
 create mode 100755 .github/hooks/session-end.sh
 create mode 100755 .github/hooks/session-start.sh
 create mode 100644 .github/secret_scanning.yml
 create mode 100644 .github/semgrep.yml
 create mode 100644 .github/workflows/copilot-setup-steps.yml
 delete mode 100644 .github/workflows/rhiza_codeql.yml
 delete mode 100644 .github/workflows/rhiza_deptry.yml
 delete mode 100644 .github/workflows/rhiza_mypy.yml
 delete mode 100644 .github/workflows/rhiza_pre-commit.yml
 delete mode 100644 .github/workflows/rhiza_validate.yml
 create mode 100644 .github/workflows/rhiza_weekly.yml
 create mode 100644 .python-version
 create mode 100644 .rhiza/assets/rhiza-logo.svg
 delete mode 100644 .rhiza/make.d/01-custom-env.mk
 delete mode 100644 .rhiza/make.d/10-custom-task.mk
 create mode 100644 .rhiza/make.d/book.mk
 create mode 100644 .rhiza/make.d/marimo.mk
 create mode 100644 .rhiza/make.d/quality.mk
 create mode 100644 .rhiza/make.d/releasing.mk
 delete mode 100644 .rhiza/requirements/tests.txt
 delete mode 100644 .rhiza/scripts/check_workflow_names.py
 delete mode 100755 .rhiza/scripts/release.sh
 create mode 100644 .rhiza/template.lock
 delete mode 100755 .rhiza/utils/version_matrix.py
 delete mode 100644 CODE_OF_CONDUCT.md
 delete mode 100644 CONTRIBUTING.md
 delete mode 100644 book/README.md
 delete mode 100644 book/book.mk
 delete mode 100644 book/marimo/marimo.mk
 delete mode 100644 book/marimo/notebooks/rhiza.py
 delete mode 100644 book/minibook-templates/custom.html.jinja2
 create mode 100644 docs/assets/rhiza-logo.svg
 rename book/marimo/README.md => docs/development/MARIMO.md (95%)
 create mode 100644 docs/index.md
 create mode 100644 docs/mkdocs-base.yml
 delete mode 100644 renovate.json

diff --git a/.github/DISCUSSION_TEMPLATE/q-and-a.yml b/.github/DISCUSSION_TEMPLATE/q-and-a.yml
new file mode 100644
index 00000000..c83b0a7d
--- /dev/null
+++ b/.github/DISCUSSION_TEMPLATE/q-and-a.yml
@@ -0,0 +1,25 @@
+title: "[Question] "
+labels: ["question"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Welcome! Use this space to ask questions, share how your use-case, or explore ideas with the community.
+
+  - type: textarea
+    id: question
+    attributes:
+      label: Your Question or Topic
+      description: What would you like to discuss?
+    validations:
+      required: true
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Context
+      description: Any relevant code, configuration, or background that helps frame your question.
+      placeholder: |
+        ```python
+        # your code snippet here
+        ```
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 00000000..060ab290
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,57 @@
+name: Bug Report
+description: Report a bug or unexpected behaviour
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report a bug. Please fill out the sections below.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: A clear and concise description of what the bug is.
+      placeholder: What happened?
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to reproduce
+      description: Minimal steps to reproduce the behaviour.
+      placeholder: |
+        1. Run `make ...`
+        2. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behaviour
+      description: What did you expect to happen?
+    validations:
+      required: true
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: |
+        Relevant versions and system info. Run `make info` if available.
+      placeholder: |
+        - OS: macOS 14 / Ubuntu 24.04 / Windows 11
+        - Python: 3.13.x
+        - rhiza version:
+    validations:
+      required: false
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Logs, screenshots, or anything else that may be helpful.
+    validations:
+      required: false
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 00000000..1b0de2d0
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,41 @@
+name: Feature Request
+description: Suggest a new feature or enhancement
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for proposing a feature. Please align with the team before investing significant effort.
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem / motivation
+      description: What problem does this solve? Why is it valuable?
+      placeholder: As a contributor I find it hard to ... because ...
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed solution
+      description: Describe the solution you have in mind.
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: Other approaches you have considered and why you ruled them out.
+    validations:
+      required: false
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Links, mockups, prior art, or anything else that may be helpful.
+    validations:
+      required: false
diff --git a/.github/actions/configure-git-auth/README.md b/.github/actions/configure-git-auth/README.md
new file mode 100644
index 00000000..4b6faeb7
--- /dev/null
+++ b/.github/actions/configure-git-auth/README.md
@@ -0,0 +1,80 @@
+# Configure Git Auth for Private Packages
+
+This composite action configures git to use token authentication for private GitHub packages.
+
+## Usage
+
+Add this step before installing dependencies that include private GitHub packages:
+
+```yaml
+- name: Configure git auth for private packages
+  uses: ./.github/actions/configure-git-auth
+  with:
+    token: ${{ secrets.GH_PAT }}
+```
+
+The `GH_PAT` secret should be a Personal Access Token with `repo` scope.
+
+## What It Does
+
+This action runs:
+
+```bash
+git config --global url."https://<token>@github.com/".insteadOf "https://github.com/"
+```
+
+This tells git to automatically inject the token into all HTTPS GitHub URLs, enabling access to private repositories.
+
+## When to Use
+
+Use this action when your project has dependencies defined in `pyproject.toml` like:
+
+```toml
+[tool.uv.sources]
+private-package = { git = "https://github.com/your-org/private-package.git", rev = "v1.0.0" }
+```
+
+## Token Requirements
+
+By default, this action will use the workflow’s built-in `GITHUB_TOKEN` (`github.token`) if no `token` input is provided or if the provided value is empty (it uses `inputs.token || github.token` internally).
+
+The `GITHUB_TOKEN` is usually sufficient when:
+
+- installing dependencies hosted in the **same repository** as the workflow, or
+- accessing **public** repositories.
+
+The default `GITHUB_TOKEN` typically does **not** have permission to read other private repositories, even within the same organization. For that scenario, you should create a Personal Access Token (PAT) with `repo` scope and store it as `secrets.GH_PAT`, then pass it to the action via the `token` input.
+
+If you configure the step as in the example (`token: ${{ secrets.GH_PAT }}`) and `secrets.GH_PAT` is not defined, GitHub Actions passes an empty string to the action. The composite action then falls back to `github.token`, so the configuration step itself still succeeds. However, any subsequent step that tries to access private repositories that are not covered by the permissions of `GITHUB_TOKEN` will fail with an authentication error.
+## Example Workflow
+
+```yaml
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Install dependencies
+        run: uv sync --frozen
+
+      - name: Run tests
+        run: uv run pytest
+```
+
+## See Also
+
+- [PRIVATE_PACKAGES.md](../../../.rhiza/docs/PRIVATE_PACKAGES.md) - Complete guide to using private packages
+- [TOKEN_SETUP.md](../../../.rhiza/docs/TOKEN_SETUP.md) - Setting up Personal Access Tokens
diff --git a/.github/actions/configure-git-auth/action.yml b/.github/actions/configure-git-auth/action.yml
new file mode 100644
index 00000000..d4d898fb
--- /dev/null
+++ b/.github/actions/configure-git-auth/action.yml
@@ -0,0 +1,21 @@
+name: 'Configure Git Auth for Private Packages'
+description: 'Configure git to use token authentication for private GitHub packages'
+
+inputs:
+  token:
+    description: 'GitHub token to use for authentication'
+    required: false
+
+runs:
+  using: composite
+  steps:
+    - name: Configure git authentication
+      shell: bash
+      env:
+        GH_TOKEN: ${{ inputs.token || github.token }}
+      run: |
+        # Configure git to use token authentication for GitHub URLs
+        # This allows uv/pip to install private packages from GitHub
+        git config --global url."https://${GH_TOKEN}@github.com/".insteadOf "https://github.com/"
+
+        echo "✓ Git configured to use token authentication for GitHub"
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 00000000..ec0580fc
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,181 @@
+# Rhiza Copilot Instructions
+
+You are working in a project that utilises the `rhiza` framework. Rhiza is a collection of reusable
+configuration templates and tooling designed to standardise and streamline modern Python development.
+
+As a Rhiza-based project, this workspace adheres to specific conventions for structure, dependency management, and automation.
+
+## Development Environment
+
+The project uses `make` and `uv` for development tasks. UV handles all dependency and Python version management automatically.
+
+### Prerequisites
+
+- **Git**: Required for version control
+- **Make**: Command runner for all development tasks
+- **curl**: Required for installing uv (usually pre-installed on most systems)
+
+**Note**: Python is NOT a prerequisite. UV will automatically download and install the correct Python version (specified in `.python-version`) when you run `make install`.
+
+### Environment Setup
+
+Setting up your environment is simple:
+
+```bash
+make install
+```
+
+This single command handles everything:
+1. Installs `uv` package manager (to `./bin/uv` if not already in PATH)
+2. Downloads and installs the correct Python version from `.python-version` (currently 3.13)
+3. Creates a `.venv` virtual environment with that Python version
+4. Installs all project dependencies from `pyproject.toml`
+
+### Verifying Installation
+
+After installation completes, verify everything works:
+
+```bash
+make test  # Should run successfully
+```
+
+### Environment Variables
+
+UV automatically uses these environment variables (set by the bootstrap process):
+- `UV_LINK_MODE=copy`: Ensures proper dependency linking across filesystems
+- `UV_VENV_CLEAR=1`: Clears existing venv on reinstall to avoid conflicts
+
+### Common Development Commands
+
+- **Install Dependencies**: `make install` (full setup: uv, Python, venv, dependencies)
+- **Run Tests**: `make test` (runs `pytest` with coverage)
+- **Format Code**: `make fmt` (runs `ruff format` and `ruff check --fix`)
+- **Check Dependencies**: `make deptry` (checks for missing/unused dependencies)
+- **Marimo Notebooks**: `make marimo` (starts the Marimo notebook server)
+- **Build Documentation**: `make book` (builds the documentation book)
+- **Clean Environment**: `make clean` (removes build artifacts and stale branches)
+
+### Troubleshooting
+
+- **Installation fails**: Check internet connectivity (UV needs to download Python and packages)
+- **Python version issues**: The `.python-version` file is the single source of truth. UV uses this automatically.
+- **Pre-commit failures**: Run `make fmt` to auto-fix most formatting issues
+- **Stale environment**: Run `make clean` followed by `make install` to start fresh
+
+### Important Notes for Agents
+
+- **Virtual Environment Activation**: Most `make` commands automatically handle virtual environment activation. Manual activation is rarely needed.
+- **Python Version**: The repository specifies Python 3.13 in `.python-version`. UV installs this automatically.
+- **All Commands Through Make**: Always use `make` targets rather than running tools directly to ensure consistency.
+- **When a `make` target exists, use it**: Do not replace `make test`, `make fmt`, `make deptry`, etc. with direct tool commands.
+- **For Python commands without a `make` target, use `uv run`**: Run Python and Python tooling via `uv run <command>`.
+- **Never call the interpreter directly from `.venv`**: Do **not** use `.venv/bin/python`, `.venv/bin/pytest`, etc.
+
+### Command Execution Policy (Strict)
+
+Use these rules in order:
+
+1. If there is an appropriate `make` target, use the `make` target.
+2. If no `make` target exists and you must run Python code/tooling, use `uv run ...`.
+3. Do not invoke binaries from `.venv/bin` directly.
+
+Examples:
+
+- ✅ `make test`
+- ✅ `make fmt`
+- ✅ `uv run pytest`
+- ✅ `uv run python -m pytest tests/property/test_makefile_properties.py`
+- ✅ `uv run python scripts/some_script.py`
+- ❌ `.venv/bin/python -m pytest`
+- ❌ `.venv/bin/pytest`
+
+### Customizing Setup with Hooks
+
+The Makefile provides hooks for customizing the setup process. Add these to the root `Makefile`:
+
+```makefile
+# Run before make install
+pre-install::
+	@echo "Installing system dependencies..."
+	@command -v graphviz || brew install graphviz
+
+# Run after make install
+post-install::
+	@echo "Running custom setup..."
+	@./scripts/custom-setup.sh
+```
+
+**Available hooks:**
+- `pre-install` / `post-install`: Runs around `make install`
+- `pre-sync` / `post-sync`: Runs around template synchronization
+- `pre-validate` / `post-validate`: Runs around validation
+- `pre-release` / `post-release`: Runs around releases
+
+**Note**: Use double-colon syntax (`::`) for hooks to allow multiple definitions. See `.rhiza/make.d/README.md` for more details.
+
+### Cloud/CI Environment Setup
+
+The Copilot coding agent environment is automatically configured via official GitHub mechanisms:
+
+- **`.github/workflows/copilot-setup-steps.yml`**: Runs before the agent starts. Installs uv, configures git auth for private packages, and runs `make install` to set up a deterministic environment.
+- **`.github/hooks/hooks.json`**: Defines session lifecycle hooks:
+  - `sessionStart`: Validates the environment is correctly set up (uv available, .venv exists)
+  - `sessionEnd`: Runs `make fmt` and `make test` as quality gates after the agent finishes work
+
+These files must exist on the default branch. The agent does not need to run any setup commands manually.
+
+For DevContainers and Codespaces, the `.devcontainer/` configuration and `bootstrap.sh` handle setup automatically.
+
+## Project Structure
+
+- `src/`: Source code
+- `tests/`: Tests (pytest)
+- `assets/`: Static assets
+- `book/`: Documentation source
+- `docker/`: Docker configuration
+- `.rhiza/`: Rhiza-specific scripts and configurations
+
+## Coding Standards
+
+- **Style**: Follow PEP 8. Use `make fmt` to enforce style.
+- **Testing**: Write tests in `tests/` using `pytest`. Ensure high coverage.
+- **Documentation**: Document code using docstrings.
+- **Dependencies**: Manage dependencies in `pyproject.toml`. Use `uv add` to add dependencies.
+
+## Workflow
+
+1.  **Setup**: Run `make install` to set up the environment.
+2.  **Develop**: Write code in `src/` and tests in `tests/`.
+3.  **Test**: Run `make test` to verify changes.
+4.  **Format**: Run `make fmt` before committing.
+5.  **Verify**: Run `make deptry` to check dependencies.
+
+## GitHub Agentic Workflows (gh-aw)
+
+This repository uses GitHub Agentic Workflows for AI-driven automation.
+Agentic workflow files are Markdown files in `.github/workflows/` with
+`.lock.yml` compiled counterparts.
+
+**Key Commands:**
+- `make gh-aw-compile` or `gh aw compile` — Compile workflow `.md` files to `.lock.yml`
+- `make gh-aw-run WORKFLOW=<name>` or `gh aw run <name>` — Run a specific workflow locally
+- `make gh-aw-status` — Check status of all agentic workflows
+- `make gh-aw-setup` — Configure secrets and engine for first-time setup
+
+**Important Rules:**
+- **Never edit `.lock.yml` files directly** — Always edit the `.md` source and recompile
+- Workflows must be compiled before they can run in GitHub Actions
+- After editing any `.md` workflow, always run `make gh-aw-compile` and commit both files
+
+**Available Starter Workflows:**
+- `daily-repo-status.md` — Daily repository health reports
+- `ci-doctor.md` — Automatic CI failure diagnosis
+- `issue-triage.md` — Automatic issue classification and labeling
+
+## Key Files
+
+- `Makefile`: Main entry point for tasks.
+- `pyproject.toml`: Project configuration and dependencies.
+- `.devcontainer/bootstrap.sh`: Bootstrap script for dev containers.
+- `.github/workflows/copilot-setup-steps.yml`: Agent environment setup (runs before agent starts).
+- `.github/hooks/hooks.json`: Agent session hooks (quality gates).
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..1da7ad10
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,80 @@
+# This file is part of the jebel-quant/rhiza repository
+# (https://github.com/jebel-quant/rhiza).
+#
+# Configuration: Dependabot
+#
+# Purpose: Automate dependency updates for Python packages, GitHub Actions, and Docker images.
+#
+# Documentation: https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Python dependencies using uv
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "tuesday"
+      time: "09:00"
+      timezone: "Asia/Dubai"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-major"]
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+      - "python"
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+        update-types:
+          - "patch"
+          - "minor"
+    commit-message:
+      prefix: "chore(deps)"
+      prefix-development: "chore(deps-dev)"
+      include: "scope"
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "tuesday"
+      time: "09:00"
+      timezone: "Asia/Dubai"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-major"]
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+      - "github-actions"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+        update-types:
+          - "patch"
+          - "minor"
+          
+    commit-message:
+      prefix: "chore(deps)"
+      include: "scope"
+
+  # Docker
+  #- package-ecosystem: "docker"
+  #  directory: "/docker"
+  #  schedule:
+  #    interval: "weekly"
+  #    day: "tuesday"
+  #    time: "09:00"
+  #    timezone: "Asia/Dubai"
+  #  open-pull-requests-limit: 10
+  #  labels:
+  #    - "dependencies"
+  #    - "docker"
+  #  commit-message:
+  #    prefix: "chore(deps)"
+  #    include: "scope"
diff --git a/.github/hooks/hooks.json b/.github/hooks/hooks.json
new file mode 100644
index 00000000..6afa9448
--- /dev/null
+++ b/.github/hooks/hooks.json
@@ -0,0 +1,21 @@
+{
+  "version": 1,
+  "hooks": {
+    "sessionStart": [
+      {
+        "type": "command",
+        "bash": ".github/hooks/session-start.sh",
+        "cwd": ".",
+        "timeoutSec": 30
+      }
+    ],
+    "sessionEnd": [
+      {
+        "type": "command",
+        "bash": ".github/hooks/session-end.sh",
+        "cwd": ".",
+        "timeoutSec": 120
+      }
+    ]
+  }
+}
diff --git a/.github/hooks/session-end.sh b/.github/hooks/session-end.sh
new file mode 100755
index 00000000..14e58557
--- /dev/null
+++ b/.github/hooks/session-end.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+set -euo pipefail
+
+# Session End Hook
+# Runs quality gates after the agent finishes work.
+
+echo "[copilot-hook] Running post-work quality gates..."
+
+# Format code
+echo "[copilot-hook] Formatting code..."
+if ! make fmt; then
+    echo "[copilot-hook] [ERROR] Formatting check failed"
+    echo "[copilot-hook] [INFO] Remediation: Review the formatting errors above"
+    echo "[copilot-hook] [INFO] Common fixes:"
+    echo "[copilot-hook]    - Run 'make fmt' locally to see detailed errors"
+    echo "[copilot-hook]    - Check for syntax errors in modified files"
+    echo "[copilot-hook]    - Ensure all files follow project style guidelines"
+    exit 1
+fi
+echo "[copilot-hook] [OK] Code formatting passed"
+
+# Run tests
+echo "[copilot-hook] Running tests..."
+if ! make test; then
+    echo "[copilot-hook] [ERROR] Tests failed"
+    echo "[copilot-hook] [INFO] Remediation: Review the test failures above"
+    echo "[copilot-hook] [INFO] Common fixes:"
+    echo "[copilot-hook]    - Run 'make test' locally to see detailed output"
+    echo "[copilot-hook]    - Check if new code broke existing functionality"
+    echo "[copilot-hook]    - Verify test assertions match expected behavior"
+    echo "[copilot-hook]    - Review test logs in _tests/ directory"
+    exit 1
+fi
+echo "[copilot-hook] [OK] Tests passed"
+
+echo "[copilot-hook] [OK] All quality gates passed"
diff --git a/.github/hooks/session-start.sh b/.github/hooks/session-start.sh
new file mode 100755
index 00000000..17e0f730
--- /dev/null
+++ b/.github/hooks/session-start.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+set -euo pipefail
+
+# Session Start Hook
+# Validates that the environment is correctly set up before the agent begins work.
+# The virtual environment should already be activated via copilot-setup-steps.yml.
+
+echo "[copilot-hook] Validating environment..."
+
+# Verify uv is available
+if ! command -v uv >/dev/null 2>&1 && [ ! -x "./bin/uv" ]; then
+    echo "[copilot-hook] [ERROR] uv not found"
+    echo "[copilot-hook] [INFO] Remediation: Run 'make install' to set up the environment"
+    echo "[copilot-hook] [INFO] Alternative: Ensure uv is in PATH or ./bin/uv exists"
+    exit 1
+fi
+echo "[copilot-hook] [OK] uv is available"
+
+# Verify virtual environment exists
+if [ ! -d ".venv" ]; then
+    echo "[copilot-hook] [ERROR] .venv not found"
+    echo "[copilot-hook] [INFO] Remediation: Run 'make install' to create the virtual environment"
+    echo "[copilot-hook] [INFO] Details: The .venv directory should contain Python dependencies"
+    exit 1
+fi
+echo "[copilot-hook] [OK] Virtual environment exists"
+
+# Verify virtual environment is on PATH (activated via copilot-setup-steps.yml)
+if ! command -v python >/dev/null 2>&1 || [[ "$(command -v python)" != *".venv"* ]]; then
+    echo "[copilot-hook] [WARN] .venv/bin is not on PATH"
+    echo "[copilot-hook] [INFO] Note: The agent may not use the correct Python version"
+    echo "[copilot-hook] [INFO] Remediation: Ensure .venv/bin is added to PATH before running the agent"
+else
+    echo "[copilot-hook] [OK] Virtual environment is activated"
+fi
+
+echo "[copilot-hook] [OK] Environment validated successfully"
diff --git a/.github/secret_scanning.yml b/.github/secret_scanning.yml
new file mode 100644
index 00000000..fdfd809c
--- /dev/null
+++ b/.github/secret_scanning.yml
@@ -0,0 +1,20 @@
+# This file is part of the jebel-quant/rhiza repository
+# (https://github.com/jebel-quant/rhiza).
+#
+# Configuration: GitHub Secret Scanning
+#
+# Purpose: Configure GitHub secret scanning to identify and prevent accidental
+#          exposure of secrets, credentials, and tokens in the repository.
+#
+# Note: Secret scanning must be enabled in repository Settings >
+#       Security > Code security and analysis > Secret scanning.
+#
+# Documentation: https://docs.github.com/en/code-security/secret-scanning/configuring-secret-scanning-for-your-repository
+
+paths-ignore:
+  # Ignore test fixtures that may contain example/fake secrets
+  - ".rhiza/tests/**"
+  - "tests/**"
+  # Ignore documentation that references example tokens/keys
+  - "docs/**/*.md"
+  - "book/**"
diff --git a/.github/semgrep.yml b/.github/semgrep.yml
new file mode 100644
index 00000000..a5cc97c6
--- /dev/null
+++ b/.github/semgrep.yml
@@ -0,0 +1,84 @@
+rules:
+  # ----------------------------
+  # Security
+  # ----------------------------
+
+  - id: numpy-load-allow-pickle
+    patterns:
+      - pattern: np.load($PATH, ...)
+      - pattern-not: np.load($PATH, ..., allow_pickle=False, ...)
+    message: |
+      np.load() may deserialize arbitrary objects when allow_pickle=True
+      (default in older NumPy versions). This can execute malicious code.
+      Pass allow_pickle=False unless explicitly required.
+    languages: [python]
+    severity: ERROR
+    metadata:
+      category: security
+      cwe: "CWE-502: Deserialization of Untrusted Data"
+
+  # ----------------------------
+  # Randomness / Reproducibility
+  # ----------------------------
+
+  - id: numpy-random-seed
+    pattern: np.random.seed(...)
+    message: |
+      np.random.seed() sets global state and is not thread-safe.
+      Prefer a local Generator via np.random.default_rng().
+    languages: [python]
+    severity: WARNING
+    metadata:
+      category: best-practice
+
+  - id: numpy-global-random-state
+    patterns:
+      - pattern-either:
+          - pattern: np.random.rand(...)
+          - pattern: np.random.randn(...)
+          - pattern: np.random.randint(...)
+          - pattern: np.random.random(...)
+          - pattern: np.random.normal(...)
+          - pattern: np.random.uniform(...)
+          - pattern: np.random.choice(...)
+          - pattern: np.random.shuffle(...)
+    message: |
+      Global np.random.* usage is not thread-safe and can harm reproducibility.
+      Prefer a local Generator:
+        rng = np.random.default_rng(seed)
+        rng.method(...)
+    languages: [python]
+    severity: INFO
+    metadata:
+      category: best-practice
+
+  # ----------------------------
+  # Numerical Stability
+  # ----------------------------
+
+  - id: numpy-avoid-inv
+    pattern: np.linalg.inv($X)
+    message: |
+      Avoid explicit matrix inversion. Use np.linalg.solve(A, b)
+      for better numerical stability and performance.
+    languages: [python]
+    severity: WARNING
+    metadata:
+      category: numerical-stability
+
+  # ----------------------------
+  # Deprecated / Dangerous APIs
+  # ----------------------------
+
+  - id: numpy-matrix-deprecated
+    patterns:
+      - pattern-either:
+          - pattern: np.matrix(...)
+          - pattern: np.mat(...)
+    message: |
+      np.matrix is deprecated and scheduled for removal. Use np.array
+      or np.ndarray instead. It has different operator semantics (*).
+    languages: [python]
+    severity: WARNING
+    metadata:
+      category: maintainability
diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
new file mode 100644
index 00000000..c54de383
--- /dev/null
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -0,0 +1,50 @@
+# This file is part of the jebel-quant/rhiza repository
+# (https://github.com/jebel-quant/rhiza).
+#
+# Workflow: Copilot Setup Steps
+#
+# Purpose: Preconfigure the development environment before the Copilot
+#          coding agent begins working. This ensures the agent always
+#          has a deterministic, fully working environment.
+#
+# Reference: https://docs.github.com/en/copilot/customizing-copilot/customizing-the-development-environment-for-copilot-coding-agent
+
+name: "(RHIZA) AGENT SETUP"
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6.0.2
+        with:
+          lfs: true
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+        with:
+          version: "0.11.6"
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Install dependencies
+        env:
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
+        run: make install
+
+      - name: Activate virtual environment
+        run: echo "${{ github.workspace }}/.venv/bin" >> "$GITHUB_PATH"
diff --git a/.github/workflows/rhiza_book.yml b/.github/workflows/rhiza_book.yml
index f8c85942..2d7612d4 100644
--- a/.github/workflows/rhiza_book.yml
+++ b/.github/workflows/rhiza_book.yml
@@ -36,33 +36,48 @@ jobs:
 
     steps:
       # Check out the repository code
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0.2
         with:
           lfs: true
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.0.0
         with:
-          version: "0.9.27"
+          version: "0.11.6"
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
 
       - name: "Sync the virtual environment for ${{ github.repository }}"
         shell: bash
         env:
-          UV_EXTRA_INDEX_URL: ${{ secrets.uv-extra-index-url }}
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
         run: |
           # will just use .python-version?
           uv sync --all-extras --all-groups --frozen
 
       - name: "Make the book"
         env:
-          UV_EXTRA_INDEX_URL: ${{ secrets.uv-extra-index-url }}
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
         run: |
-          make -f .rhiza/rhiza.mk book
+          make book
+
+      # Step 5a: Upload the book as a downloadable workflow artifact
+      # This allows anyone to download the built documentation directly from
+      # GitHub Actions without needing to run a full local build.
+      - name: Upload book as workflow artifact
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: book
+          path: _book/
+          retention-days: 30
 
-      # Step 5: Package all artifacts for GitHub Pages deployment
+      # Step 5b: Package all artifacts for GitHub Pages deployment
       # This prepares the combined outputs for deployment by creating a single artifact
       - name: Upload static files as artifact
-        uses: actions/upload-pages-artifact@v4  # Official GitHub Pages artifact upload action
+        uses: actions/upload-pages-artifact@v5.0.0  # Official GitHub Pages artifact upload action
         with:
           path: _book/  # Path to the directory containing all artifacts to deploy
 
@@ -73,5 +88,5 @@ jobs:
       # If PUBLISH_COMPANION_BOOK is not set, it defaults to allowing deployment
       - name: Deploy to GitHub Pages
         if: ${{ !github.event.repository.fork && (vars.PUBLISH_COMPANION_BOOK == 'true' || vars.PUBLISH_COMPANION_BOOK == '') }}
-        uses: actions/deploy-pages@v4  # Official GitHub Pages deployment action
+        uses: actions/deploy-pages@v5.0.0  # Official GitHub Pages deployment action
         continue-on-error: true
diff --git a/.github/workflows/rhiza_codeql.yml b/.github/workflows/rhiza_codeql.yml
deleted file mode 100644
index aca6b23b..00000000
--- a/.github/workflows/rhiza_codeql.yml
+++ /dev/null
@@ -1,125 +0,0 @@
-# For most projects, this workflow file will not need changing; you simply need
-# to commit it to your repository.
-#
-# You may wish to alter this file to override the set of languages analyzed,
-# or to provide custom queries or build logic.
-#
-# ******** NOTE ********
-# We have attempted to detect the languages in your repository. Please check
-# the `language` matrix defined below to confirm you have the correct set of
-# supported CodeQL languages.
-#
-# ******** IMPORTANT: GitHub Advanced Security Required ********
-# CodeQL is FREE for public repositories, but requires GitHub Advanced Security
-# (part of GitHub Enterprise) for private repositories.
-#
-# This workflow automatically:
-# - Runs on public repositories
-# - Skips on private repositories (unless Advanced Security is available)
-#
-# To control this behavior, set the CODEQL_ENABLED repository variable:
-# - Set to 'true' to force enable (if you have Advanced Security on private repos)
-# - Set to 'false' to disable entirely
-# - Leave unset for automatic behavior (recommended)
-#
-# For more information, see docs/CUSTOMIZATION.md
-#
-name: "(RHIZA) CODEQL"
-
-on:
-  push:
-    branches: [ "main", "master" ]
-  pull_request:
-    branches: [ "main", "master" ]
-  schedule:
-    - cron: '27 1 * * 1'
-
-jobs:
-  analyze:
-    name: Analyze (${{ matrix.language }})
-    # Runner size impacts CodeQL analysis time. To learn more, please see:
-    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
-    #   - https://gh.io/supported-runners-and-hardware-resources
-    #   - https://gh.io/using-larger-runners (GitHub.com only)
-    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
-    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
-    # CodeQL requires GitHub Advanced Security (part of GitHub Enterprise).
-    # For users without Enterprise license:
-    # - Public repositories: CodeQL is available for free
-    # - Private repositories: Requires GitHub Advanced Security
-    # To disable this workflow, set CODEQL_ENABLED repository variable to 'false'
-    # To enable this workflow for private repos with Advanced Security, set CODEQL_ENABLED to 'true'
-    if: |
-      vars.CODEQL_ENABLED == 'true' ||
-      (vars.CODEQL_ENABLED != 'false' && github.event.repository.visibility == 'public')
-    permissions:
-      # required for all workflows
-      security-events: write
-
-      # required to fetch internal or private CodeQL packs
-      packages: read
-
-      # only required for workflows in private repositories
-      actions: read
-      contents: read
-
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-        - language: actions
-          build-mode: none
-        - language: python
-          build-mode: none
-        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
-        # Use `c-cpp` to analyze code written in C, C++ or both
-        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
-        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
-        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
-        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
-        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
-        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v6
-
-    # Add any setup steps before running the `github/codeql-action/init` action.
-    # This includes steps like installing compilers or runtimes (`actions/setup-node`
-    # or others). This is typically only required for manual builds.
-    # - name: Setup runtime (example)
-    #   uses: actions/setup-example@v1
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4
-      with:
-        languages: ${{ matrix.language }}
-        build-mode: ${{ matrix.build-mode }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-
-        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
-
-    # If the analyze step fails for one of the languages you are analyzing with
-    # "We were unable to automatically build your code", modify the matrix above
-    # to set the build mode to "manual" for that language. Then modify this step
-    # to build your code.
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
-    - name: Run manual build steps
-      if: matrix.build-mode == 'manual'
-      shell: bash
-      run: |
-        echo 'If you are using a "manual" build mode for one or more of the' \
-          'languages you are analyzing, replace this with the commands to build' \
-          'your code, for example:'
-        echo '  make bootstrap'
-        echo '  make release'
-        exit 1
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4
-      with:
-        category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/rhiza_deptry.yml b/.github/workflows/rhiza_deptry.yml
deleted file mode 100644
index eefc2223..00000000
--- a/.github/workflows/rhiza_deptry.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-# This file is part of the jebel-quant/rhiza repository
-# (https://github.com/jebel-quant/rhiza).
-#
-# Workflow: Deptry
-#
-# Purpose: This workflow identifies missing and obsolete dependencies in the project.
-#          It helps maintain a clean dependency tree by detecting unused packages and
-#          implicit dependencies that should be explicitly declared.
-#
-# Trigger: This workflow runs on every push and on pull requests to main/master
-#          branches (including from forks)
-
-name: "(RHIZA) DEPTRY"
-
-# Permissions: Only read access to repository contents is needed
-permissions:
-    contents: read
-
-on:
-  push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
-
-jobs:
-  deptry:
-    name: Check dependencies with deptry
-    runs-on: ubuntu-latest
-    container:
-      image: ghcr.io/astral-sh/uv:0.9.27-python3.12-trixie
-
-    steps:
-      - uses: actions/checkout@v6
-
-      - name: Run deptry
-        run: make -f .rhiza/rhiza.mk deptry
-        # NOTE: make deptry is good style because it encapsulates the folders to check
-        # (e.g. src and book/marimo) and keeps CI in sync with local development.
-        # Since we use a 'uv' container, the Makefile is optimised to use the
-        # pre-installed 'uv' and 'uvx' from the system PATH.
diff --git a/.github/workflows/rhiza_marimo.yml b/.github/workflows/rhiza_marimo.yml
index 67dfda97..cf1677e8 100644
--- a/.github/workflows/rhiza_marimo.yml
+++ b/.github/workflows/rhiza_marimo.yml
@@ -34,7 +34,7 @@ jobs:
       notebook-list: ${{ steps.notebooks.outputs.matrix }}
     steps:
       # Check out the repository code
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0.2
 
       # Find all Python files in the marimo folder and create a matrix for parallel execution
       - name: Find notebooks and build matrix
@@ -75,20 +75,34 @@ jobs:
     name: Run notebook ${{ matrix.notebook }}
     steps:
       # Check out the repository code
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0.2
         with:
           lfs: true
 
       # Install uv/uvx
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.0.0
         with:
-          version: "0.9.27"
+          version: "0.11.6"
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
 
       # Execute the notebook with the appropriate runner based on its content
       - name: Run notebook
+        id: artefact-folder
+        env:
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
         run: |
-          uvx uv run "${{ matrix.notebook }}"
+          notebook="${{ matrix.notebook }}"
+          notebook_stem="$(basename "$notebook" .py)"
+          artefact_folder="results/${notebook_stem}"
+          mkdir -p "${artefact_folder}"
+          echo "name=${notebook_stem}" >> "$GITHUB_OUTPUT"
+          export NOTEBOOK_OUTPUT_FOLDER="${artefact_folder}"
+          uvx uv run "$notebook"
           # uvx → creates a fresh ephemeral environment
           # uv run → runs the notebook as a script in that ephemeral env
           # No project packages are pre-installed
@@ -99,3 +113,11 @@ jobs:
           # Catches missing uv install or pip steps early
           # Ensures CI/other users can run the notebook without manual setup
         shell: bash
+
+      - name: Upload notebook artefacts
+        if: always()
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: notebook-artefacts-${{ steps.artefact-folder.outputs.name }}
+          path: results/${{ steps.artefact-folder.outputs.name }}/
+          if-no-files-found: ignore
diff --git a/.github/workflows/rhiza_mypy.yml b/.github/workflows/rhiza_mypy.yml
deleted file mode 100644
index 011e558d..00000000
--- a/.github/workflows/rhiza_mypy.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-# This file is part of the jebel-quant/rhiza repository
-# (https://github.com/jebel-quant/rhiza).
-#
-# Workflow: Mypy
-#
-# Purpose: Run static type checking with mypy in strict mode to ensure
-#          type safety across the codebase.
-#
-# Trigger: On push and pull requests to main/master branches.
-
-name: "(RHIZA) MYPY"
-
-permissions:
-  contents: read
-
-on:
-  push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
-
-jobs:
-  mypy:
-    name: Static type checking with mypy
-    runs-on: ubuntu-latest
-    container:
-      image: ghcr.io/astral-sh/uv:0.9.27-python3.12-trixie
-
-    steps:
-      - uses: actions/checkout@v6
-
-      # to brutal for now
-      # - name: Run mypy
-      #   run: make -f .rhiza/rhiza.mk mypy
diff --git a/.github/workflows/rhiza_pre-commit.yml b/.github/workflows/rhiza_pre-commit.yml
deleted file mode 100644
index 4190d4d9..00000000
--- a/.github/workflows/rhiza_pre-commit.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# This file is part of the jebel-quant/rhiza repository
-# (https://github.com/jebel-quant/rhiza).
-#
-# Workflow: Pre-commit
-#
-# Purpose: This workflow runs pre-commit checks to ensure code quality
-#          and consistency across the codebase. It helps catch issues
-#          like formatting errors, linting issues, and other code quality
-#          problems before they are merged.
-#
-# Trigger: This workflow runs on every push and on pull requests to main/master
-#          branches (including from forks)
-#
-# Components:
-#   - 🔍 Run pre-commit checks using reusable action
-
-name: "(RHIZA) PRE-COMMIT"
-permissions:
-  contents: read
-
-on:
-  push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v6
-
-      # Run pre-commit
-      - name: Run pre-commit
-        run: |
-          make -f .rhiza/rhiza.mk fmt
diff --git a/.github/workflows/rhiza_release.yml b/.github/workflows/rhiza_release.yml
index 7b1abf73..3146205c 100644
--- a/.github/workflows/rhiza_release.yml
+++ b/.github/workflows/rhiza_release.yml
@@ -7,11 +7,19 @@
 #
 # 📋 Pipeline Phases:
 #   1. 🔍 Validate Tag - Check tag format and ensure release doesn't already exist
-#   2. 🏗️ Build - Build Python package with Hatch (if [build-system] is defined in pyproject.toml
-#   3. 📝 Draft Release - Create draft GitHub release with build artifacts
-#   4. 🚀 Publish to PyPI - Publish package using OIDC or custom feed
-#   5. 🐳 Publish Devcontainer - Build and publish devcontainer image (conditional)
-#   6. ✅ Finalize Release - Publish the GitHub release with links
+#   2. 🏗️ Build - Build Python package with Hatch (if [build-system] is defined in pyproject.toml)
+#   3. 📦 Generate SBOM - Create Software Bill of Materials (CycloneDX format)
+#   4. 📝 Draft Release - Create draft GitHub release with build artifacts and SBOM
+#   5. 🚀 Publish to PyPI - Publish package using OIDC or custom feed
+#   6. 🐳 Publish Devcontainer - Build and publish devcontainer image (conditional)
+#   7. ✅ Finalize Release - Publish the GitHub release with links
+#
+# 📦 SBOM Generation:
+#   - Generated using CycloneDX format (industry standard for software supply chain security)
+#   - Creates both JSON and XML formats for maximum compatibility
+#   - SBOM attestations are created and stored (public repos only)
+#   - Attached to GitHub releases for transparency and compliance
+#   - Skipped if pyproject.toml doesn't exist
 #
 # 🐳 Devcontainer Publishing:
 #   - Only occurs when PUBLISH_DEVCONTAINER repository variable is set to "true"
@@ -33,7 +41,8 @@
 #   - No PyPI credentials stored; relies on Trusted Publishing via GitHub OIDC
 #   - For custom feeds, PYPI_TOKEN secret is used with default username __token__
 #   - Container registry uses GITHUB_TOKEN for authentication
-#   - SLSA provenance attestations generated for build artifacts (supply chain security)
+#   - SLSA provenance attestations generated for build artifacts (public repos only)
+#   - SBOM attestations generated for supply chain transparency (public repos only)
 #
 # 📄 Requirements:
 #   - pyproject.toml with top-level version field (for Python packages)
@@ -65,7 +74,7 @@ permissions:
   contents: write       # Needed to create releases
   id-token: write       # Needed for OIDC authentication with PyPI
   packages: write       # Needed to publish devcontainer image
-  attestations: write   # Needed for SLSA provenance attestations
+  attestations: write   # Needed for SLSA provenance attestations (public repos only)
 
 jobs:
   tag:
@@ -75,7 +84,7 @@ jobs:
       tag: ${{ steps.set_tag.outputs.tag }}
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0
 
@@ -106,21 +115,19 @@ jobs:
     needs: tag
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.0.0
         with:
-          version: "0.9.27"
+          version: "0.11.6"
 
-      - name: "Sync the virtual environment for ${{ github.repository }}"
-        shell: bash
-        run: |
-          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
-          # will just use .python-version?
-          uv sync --all-extras --all-groups --frozen
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
 
       - name: Verify version matches tag
         if: hashFiles('pyproject.toml') != ''
@@ -129,11 +136,16 @@ jobs:
           TAG_VERSION=${TAG_VERSION#v}
           PROJECT_VERSION=$(uv version --short)
 
-          if [[ "$PROJECT_VERSION" != "$TAG_VERSION" ]]; then
-            echo "::error::Version mismatch: pyproject.toml has '$PROJECT_VERSION' but tag is '$TAG_VERSION'"
+          # Normalize tag version to PEP 440 format for comparison.
+          # Tags use semver format (e.g., 0.11.1-beta.1) while uv version --short
+          # returns PEP 440 normalized format (e.g., 0.11.1b1).
+          NORMALIZED_TAG=$(uv run --with packaging --no-project python3 -c "from packaging.version import Version; print(Version('$TAG_VERSION'))")
+
+          if [[ "$PROJECT_VERSION" != "$NORMALIZED_TAG" ]]; then
+            echo "::error::Version mismatch: pyproject.toml has '$PROJECT_VERSION' but tag is '$NORMALIZED_TAG' (from tag '$TAG_VERSION')"
             exit 1
           fi
-          echo "Version verified: $PROJECT_VERSION matches tag"
+          echo "Version verified: $PROJECT_VERSION matches tag (normalized: $NORMALIZED_TAG)"
 
       - name: Detect buildable Python package
         id: buildable
@@ -148,17 +160,58 @@ jobs:
         if: steps.buildable.outputs.buildable == 'true'
         run: |
           printf "[INFO] Building package...\n"
-          uvx hatch build
+          uv build
+
+      - name: Install Python for SBOM generation
+        if: hashFiles('pyproject.toml') != ''
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version-file: .python-version
+
+      - name: Sync environment for SBOM generation
+        if: hashFiles('pyproject.toml') != ''
+        run: |
+          export UV_EXTRA_INDEX_URL="${{ secrets.UV_EXTRA_INDEX_URL }}"
+          uv sync --all-extras --all-groups --frozen
+
+      - name: Generate SBOM (CycloneDX)
+        if: hashFiles('pyproject.toml') != ''
+        run: |
+          printf "[INFO] Generating SBOM in CycloneDX format...\n"
+          # Note: uvx caches the tool environment, so the second call is fast
+          uvx --from 'cyclonedx-bom>=7.0.0' cyclonedx-py environment --pyproject pyproject.toml --of JSON -o sbom.cdx.json
+          uvx --from 'cyclonedx-bom>=7.0.0' cyclonedx-py environment --pyproject pyproject.toml --of XML -o sbom.cdx.xml
+          printf "[INFO] SBOM generation complete\n"
+          printf "Generated files:\n"
+          ls -lh sbom.cdx.*
+
+      - name: Attest SBOM
+        # Attest only the JSON format as it's the canonical machine-readable format.
+        # The XML format is provided for compatibility but doesn't need separate attestation.
+        if: hashFiles('pyproject.toml') != '' && github.event.repository.private == false
+        uses: actions/attest@v4.1.0
+        with:
+          subject-path: sbom.cdx.json
+          sbom-path: sbom.cdx.json
+
+      - name: Upload SBOM artifacts
+        if: hashFiles('pyproject.toml') != ''
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: sbom
+          path: |
+            sbom.cdx.json
+            sbom.cdx.xml
 
       - name: Generate SLSA provenance attestations
-        if: steps.buildable.outputs.buildable == 'true'
-        uses: actions/attest-build-provenance@v3
+        if: steps.buildable.outputs.buildable == 'true' && github.event.repository.private == false
+        uses: actions/attest-build-provenance@v4
         with:
           subject-path: dist/*
 
       - name: Upload dist artifact
         if: steps.buildable.outputs.buildable == 'true'
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7.0.1
         with:
           name: dist
           path: dist
@@ -170,13 +223,34 @@ jobs:
     needs: [tag, build]
 
     steps:
+      - name: Checkout Code
+        uses: actions/checkout@v6.0.2
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+
+      - name: Generate release notes with git-cliff
+        run: uvx git-cliff --latest --output RELEASE_NOTES.md
+
+      - name: Download SBOM artifact
+        # Downloads sbom.cdx.json and sbom.cdx.xml into sbom/ directory
+        uses: actions/download-artifact@v8.0.1
+        with:
+          name: sbom
+          path: sbom
+        continue-on-error: true
+
       - name: Create GitHub Release with artifacts
-        uses: softprops/action-gh-release@v2.5.0
+        uses: ncipollo/release-action@v1.21.0
         with:
-          tag_name: ${{ needs.tag.outputs.tag }}
+          tag: ${{ needs.tag.outputs.tag }}
           name: ${{ needs.tag.outputs.tag }}
-          generate_release_notes: true
+          bodyFile: RELEASE_NOTES.md
           draft: true
+          allowUpdates: true
+          artifacts: "sbom/*"
 
   # Decide at step-level whether to publish
   pypi:
@@ -189,12 +263,12 @@ jobs:
 
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0
 
       - name: Download dist artifact
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8.0.1
         with:
           name: dist
           path: dist
@@ -237,7 +311,7 @@ jobs:
       image_name: ${{ steps.image_name.outputs.image_name }}
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0
 
@@ -266,7 +340,7 @@ jobs:
 
       - name: Login to Container Registry
         if: steps.check_publish.outputs.should_publish == 'true'
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4.1.0
         with:
           registry: ${{ steps.registry.outputs.registry }}
           username: ${{ github.repository_owner }}
@@ -322,24 +396,24 @@ jobs:
     if: needs.pypi.result == 'success' || needs.devcontainer.result == 'success'
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
         with:
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.0.0
         with:
-          version: "0.9.27"
+          version: "0.11.6"
 
       - name: "Sync the virtual environment for ${{ github.repository }}"
         shell: bash
         run: |
-          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
+          export UV_EXTRA_INDEX_URL="${{ secrets.uv_extra_index_url }}"
           # will just use .python-version?
           uv sync --all-extras --all-groups --frozen
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v6.2.0
 
       - name: Generate Devcontainer Link
         id: devcontainer_link
@@ -358,7 +432,7 @@ jobs:
         id: pypi_link
         if: needs.pypi.outputs.should_publish == 'true' && needs.pypi.result == 'success'
         run: |
-          PACKAGE_NAME=$(python3 -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['name'])")
+          PACKAGE_NAME=$(uv run python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['name'])")
           VERSION="${{ needs.tag.outputs.tag }}"
           VERSION=${VERSION#v}
 
@@ -380,12 +454,21 @@ jobs:
           } >> "$GITHUB_OUTPUT"
 
       - name: Publish Release
-        uses: softprops/action-gh-release@v2.5.0
-        with:
-          tag_name: ${{ needs.tag.outputs.tag }}
-          draft: false
-          append_body: true
-          body: |
-            ${{ steps.devcontainer_link.outputs.message }}
-            ${{ steps.pypi_link.outputs.message }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          TAG: ${{ needs.tag.outputs.tag }}
+          DEVCONTAINER_MSG: ${{ steps.devcontainer_link.outputs.message }}
+          PYPI_MSG: ${{ steps.pypi_link.outputs.message }}
+        run: |
+          # Get existing auto-generated release notes (gracefully handle missing release)
+          EXISTING=$(gh release view "$TAG" --json body --jq '.body // ""' 2>/dev/null || echo "")
+
+          # Append links to release body
+          {
+            printf '%s' "$EXISTING"
+            [ -n "$DEVCONTAINER_MSG" ] && printf '\n\n%s' "$DEVCONTAINER_MSG"
+            [ -n "$PYPI_MSG" ] && printf '\n\n%s' "$PYPI_MSG"
+          } > /tmp/notes.md
+
+          gh release edit "$TAG" --draft=false --notes-file /tmp/notes.md
 
diff --git a/.github/workflows/rhiza_sync.yml b/.github/workflows/rhiza_sync.yml
index ea218eaf..2da8d0ed 100644
--- a/.github/workflows/rhiza_sync.yml
+++ b/.github/workflows/rhiza_sync.yml
@@ -1,32 +1,112 @@
 name: (RHIZA) SYNC
-# This workflow synchronizes the repository with its template.
-# IMPORTANT: When workflow files (.github/workflows/rhiza_*.yml) are modified,
-# a Personal Access Token (PAT) with 'workflow' scope is required.
-# The PAT_TOKEN secret must be set in repository secrets.
-# See .github/rhiza/TOKEN_SETUP.md for setup instructions.
+# Synchronizes the repository with its rhiza template.
+# - On Renovate/rhiza branch push: auto-commits synced files directly to the branch.
+# - On schedule/dispatch: opens a pull request with the synced changes.
+#
+# IMPORTANT: A PAT with 'workflow' scope (PAT_TOKEN) is required when workflow
+# files are modified. See .rhiza/docs/TOKEN_SETUP.md for setup instructions.
 
 permissions:
   contents: write
   pull-requests: write
 
 on:
+  push:
+    branches:
+      - 'renovate/jebel-quant-rhiza-**'
+      - 'rhiza/**'
+    paths:
+      - '.rhiza/template.yml'
+  schedule:
+    - cron: '0 0 * * 1'  # Weekly on Monday
   workflow_dispatch:
     inputs:
       create-pr:
         description: "Create a pull request"
         type: boolean
         default: true
-  schedule:
-    - cron: '0 0 * * 1'  # Weekly on Monday
 
 jobs:
-  sync:
-    if: ${{ github.repository != 'jebel-quant/rhiza' }}
+  sync-direct:
+    name: Sync and commit (Renovate)
+    if: github.event_name == 'push' && github.repository != 'jebel-quant/rhiza'
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v6.0.2
+        with:
+          ref: ${{ github.ref }}
+          token: ${{ secrets.PAT_TOKEN || github.token }}
+
+      - name: Check PAT_TOKEN configuration
+        shell: bash
+        env:
+          PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+        run: |
+          if [ -z "$PAT_TOKEN" ]; then
+            echo "::warning::PAT_TOKEN secret is not configured."
+            echo "::warning::If this sync modifies workflow files, the push will fail."
+            echo "::warning::See .rhiza/docs/TOKEN_SETUP.md for setup instructions."
+          else
+            echo "✓ PAT_TOKEN is configured."
+          fi
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+
+      - name: Get Rhiza version
+        id: rhiza-version
+        run: |
+          VERSION=$(cat .rhiza/.rhiza-version 2>/dev/null || echo "0.9.0")
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+
+      - name: Sync rhiza template
+        id: sync
+        run: |
+          set -euo pipefail
+
+          RHIZA_VERSION="${{ steps.rhiza-version.outputs.version }}"
+
+          echo "Running rhiza sync with version >=${RHIZA_VERSION}"
+          uvx "rhiza>=${RHIZA_VERSION}" sync .
+
+          if git diff --quiet; then
+            echo "No changes detected after template sync"
+            echo "changes=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          echo "Template changes detected"
+          echo "changes=true" >> "$GITHUB_OUTPUT"
+
+      - name: Commit and push changes
+        if: steps.sync.outputs.changes == 'true'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --global url."https://x-access-token:${{ secrets.PAT_TOKEN || github.token }}@github.com/".insteadOf "https://github.com/"
+
+          git add -A
+          git commit -m "$(cat <<'EOF'
+          chore: sync rhiza template files
+
+          Automatically synced template files after updating .rhiza/template.yml
+
+          Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
+          EOF
+          )"
+
+          git push
+
+  sync-pr:
+    name: Sync and open PR (scheduled/manual)
+    if: github.event_name != 'push' && github.repository != 'jebel-quant/rhiza'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6.0.2
         with:
           token: ${{ secrets.PAT_TOKEN || github.token }}
           fetch-depth: 0
@@ -44,13 +124,13 @@ jobs:
           if [ -z "$PAT_TOKEN" ]; then
             echo "::warning::PAT_TOKEN secret is not configured."
             echo "::warning::If this sync modifies workflow files, the push will fail."
-            echo "::warning::See .github/TOKEN_SETUP.md for setup instructions."
+            echo "::warning::See .rhiza/docs/TOKEN_SETUP.md for setup instructions."
           else
             echo "✓ PAT_TOKEN is configured."
           fi
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.0.0
 
       - name: Get Rhiza version
         id: rhiza-version
@@ -66,7 +146,7 @@ jobs:
 
           RHIZA_VERSION="${{ steps.rhiza-version.outputs.version }}"
 
-          uvx "rhiza>=${RHIZA_VERSION}" materialize --force .
+          uvx "rhiza>=${RHIZA_VERSION}" sync .
 
           git add -A
 
@@ -82,19 +162,19 @@ jobs:
 
           git config user.name  "github-actions[bot]"
           git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git config --global url."https://x-access-token:${{ secrets.PAT_TOKEN }}@github.com/".insteadOf "https://github.com/"
+          git config --global url."https://x-access-token:${{ secrets.PAT_TOKEN || github.token }}@github.com/".insteadOf "https://github.com/"
 
           git commit -m "chore: Update via rhiza"
-          
+
       - name: Create pull request
         if: >
           (github.event_name == 'schedule' || inputs.create-pr == true)
           && steps.sync.outputs.changes_detected == 'true'
-        uses: peter-evans/create-pull-request@v8
+        uses: peter-evans/create-pull-request@v8.1.1
         with:
           token: ${{ secrets.PAT_TOKEN || github.token }}
           base: ${{ github.event.repository.default_branch }}
           branch: ${{ steps.branch.outputs.name }}
           delete-branch: true
           title: "chore: Sync with rhiza"
-          body-path: ${{ runner.temp }}/pr-description.md
\ No newline at end of file
+          body-path: ${{ runner.temp }}/pr-description.md
diff --git a/.github/workflows/rhiza_validate.yml b/.github/workflows/rhiza_validate.yml
deleted file mode 100644
index d6f4640c..00000000
--- a/.github/workflows/rhiza_validate.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: (RHIZA) VALIDATE
-
-permissions:
-  contents: read
-
-on:
-  push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
-
-jobs:
-  validation:
-    runs-on: ubuntu-latest
-    # don't run this in rhiza itself. Rhiza has no template.yml file.
-    if: ${{ github.repository != 'jebel-quant/rhiza' }}
-    container:
-      image: ghcr.io/astral-sh/uv:0.9.27-python3.12-trixie
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v6
-
-      - name: Validate Rhiza config
-        shell: bash
-        run: |
-          uvx "rhiza>=0.8.0" validate .
diff --git a/.github/workflows/rhiza_weekly.yml b/.github/workflows/rhiza_weekly.yml
new file mode 100644
index 00000000..589dc9c5
--- /dev/null
+++ b/.github/workflows/rhiza_weekly.yml
@@ -0,0 +1,118 @@
+name: "(RHIZA) WEEKLY"
+
+# Runs weekly checks that are too slow or noisy for every push:
+#
+#   dep-compat-test  — Resolves all dependencies fresh (ignoring the lockfile)
+#                      and runs the full test suite. Catches newly-released
+#                      packages that break compatibility before Renovate picks
+#                      them up. Runs on schedule/dispatch only.
+#
+#   link-check       — Verifies that all hyperlinks in README.md are reachable.
+#                      Runs on schedule/dispatch only.
+
+permissions:
+  contents: read
+
+on:
+  #push:
+  #  branches: [main]
+  #  paths: [README.md]
+  #pull_request:
+  #  paths: [README.md]
+  schedule:
+    - cron: "0 8 * * 1"  # Every Monday at 08:00 UTC
+  workflow_dispatch:
+
+jobs:
+  dep-compat-test:
+    name: Test with latest compatible dependencies
+    runs-on: ubuntu-latest
+    #if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6.0.2
+        with:
+          lfs: true
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+        with:
+          version: "0.11.6"
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Resolve and install latest compatible dependencies
+        env:
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
+        run: |
+          # --upgrade ignores the committed lockfile and resolves the newest
+          # versions that satisfy pyproject.toml constraints.
+          uv sync --upgrade
+
+      - name: Show resolved package versions
+        run: |
+          echo "=== Installed package versions ==="
+          uv pip list
+
+      - name: Run tests
+        env:
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
+        run: make test
+
+  semgrep:
+    name: Semgrep (numpy)
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+        with:
+          version: "0.11.6"
+
+      - name: Configure git auth for private packages
+        uses: ./.github/actions/configure-git-auth
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Run Semgrep
+        env:
+          UV_EXTRA_INDEX_URL: ${{ secrets.UV_EXTRA_INDEX_URL }}
+        run: make semgrep
+
+  pip-audit:
+    name: Dependency vulnerability scan
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+        with:
+          version: "0.11.6"
+
+      - name: Run pip-audit
+        run: uvx pip-audit
+
+  link-check:
+    name: Check links in README.md
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Check links in README.md
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: >-
+            --verbose
+            --no-progress
+            --accept 200,206,429
+            README.md
+          fail: true
diff --git a/.gitignore b/.gitignore
index c0c30e2e..0dc346a2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,10 @@
 .idea
 .venv
 .ruff_cache
+.ty_cache
+
+# HTML outputs from docstring examples (e.g. report.save("output/..."))
+output/
 
 ### Don't expose API keys, etc.
 .env
@@ -11,9 +15,23 @@ __marimo__
 _tests
 _book
 _pdoc
+docs/notebooks/*.html
+docs/reports
+docs/notebooks.md
+docs/reports.md
 _marimushka
+_mkdocs
 _benchmarks
 _jupyter
+_site
+
+# LaTeX build artifacts
+docs/paper/*.aux
+docs/paper/*.fdb_latexmk
+docs/paper/*.fls
+docs/paper/*.log
+docs/paper/*.out
+docs/paper/*.toc
 
 # temp file used by Junie
 .output.txt
@@ -74,9 +92,13 @@ coverage.json
 *.cover
 *.py,cover
 .hypothesis/
+.benchmarks/
 .pytest_cache/
 cover/
 
+# Security scanning baselines (regenerate as needed)
+.bandit-baseline.json
+
 # Translations
 *.mo
 *.pot
@@ -97,3 +119,5 @@ cython_debug/
 # Makefile
 local.mk
 
+.bandit-baseline.json
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 07bb360e..774f3124 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,9 +7,11 @@ repos:
     hooks:
       - id: check-toml
       - id: check-yaml
+        args: ['--unsafe']
+        exclude: ^recipe/meta\.yaml$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.14.14'
+    rev: 'v0.15.10'
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix, --unsafe-fixes ]
@@ -18,13 +20,13 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.47.0
+    rev: v0.48.0
     hooks:
       - id: markdownlint
         args: ["--disable", "MD013"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.1
+    rev: 0.37.1
     hooks:
       - id: check-renovate
         args: [ "--verbose" ]
@@ -33,33 +35,34 @@ repos:
         args: ["--verbose"]
 
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.10
+    rev: v1.7.12
     hooks:
       - id: actionlint
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.24.1
+    rev: v0.25
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.9.3
+    rev: 1.9.4
     hooks:
       - id: bandit
-        args: ["--skip", "B101", "--exclude", ".venv,tests,.git,.pytest_cache"]
+        args: ["--skip", "B101", "--exclude", ".venv,tests,.rhiza/tests,.git,.pytest_cache", "-c", "pyproject.toml"]
 
-  - repo: local
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.11.6
     hooks:
-      - id: update-readme-help
-        name: Update README with Makefile help output
-        entry: make readme
-        language: system
-        files: '^Makefile$'
-        pass_filenames: false
+      - id: uv-lock
 
+  - repo: https://github.com/Jebel-Quant/rhiza-hooks
+    rev: v0.3.2  # Use the latest release
+    hooks:
+      # Migrated from rhiza
       - id: check-rhiza-workflow-names
-        name: Check and Fix Rhiza workflow names
-        entry: python .rhiza/scripts/check_workflow_names.py
-        language: python
-        additional_dependencies: [PyYAML]
-        files: ^\.github/workflows/rhiza_.*\.ya?ml$
+      - id: update-readme-help
+      # Additional utility hooks
+      - id: check-rhiza-config
+      - id: check-makefile-targets
+      - id: check-python-version-consistency
+      # - id: check-template-bundles
diff --git a/.python-version b/.python-version
new file mode 100644
index 00000000..fdcfcfdf
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.12
\ No newline at end of file
diff --git a/.rhiza/.cfg.toml b/.rhiza/.cfg.toml
index 65660d1d..c96b1dd1 100644
--- a/.rhiza/.cfg.toml
+++ b/.rhiza/.cfg.toml
@@ -1,12 +1,12 @@
 [tool.bumpversion]
-parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[a-z]+)\\.(?P<pre_n>\\d+))?(?:\\+build\\.(?P<build_n>\\d+))?"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:[-]?(?P<release>[a-z]+)[\\.]?(?P<pre_n>\\d+))?(?:\\+build\\.(?P<build_n>\\d+))?"
 serialize = ["{major}.{minor}.{patch}-{release}.{pre_n}+build.{build_n}", "{major}.{minor}.{patch}+build.{build_n}", "{major}.{minor}.{patch}-{release}.{pre_n}", "{major}.{minor}.{patch}"]
 search = "{current_version}"
 replace = "{new_version}"
 regex = false
 ignore_missing_version = false
 ignore_missing_files = false
-tag = false
+tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
@@ -14,13 +14,16 @@ allow_dirty = false
 commit = true
 message = "Chore: bump version {current_version} → {new_version}"
 commit_args = ""
+pre_commit_hooks = ["uv sync", "git add uv.lock"] # Ensure uv.lock is updated
 
 [tool.bumpversion.parts.release]
 optional_value = "prod"
 values = [
     "dev",
     "alpha",
+    "a",  # PEP 440 short form for alpha
     "beta",
+    "b",  # PEP 440 short form for beta
     "rc",
     "prod"
 ]
@@ -29,8 +32,3 @@ values = [
 filename = "pyproject.toml"
 search = 'version = "{current_version}"'
 replace = 'version = "{new_version}"'
-
-[[tool.bumpversion.files]]
-filename = "uv.lock"
-search = 'version = "{current_version}"'
-replace = 'version = "{new_version}"'
\ No newline at end of file
diff --git a/.rhiza/.env b/.rhiza/.env
index 47753265..47ca6b05 100644
--- a/.rhiza/.env
+++ b/.rhiza/.env
@@ -1,13 +1,2 @@
-MARIMO_FOLDER=book/marimo/notebooks
+MARIMO_FOLDER=docs/notebooks
 SOURCE_FOLDER=src
-SCRIPTS_FOLDER=.rhiza/scripts
-
-# Book-specific variables
-BOOK_TITLE=Project Documentation
-BOOK_SUBTITLE=Generated by minibook
-PDOC_TEMPLATE_DIR=book/pdoc-templates
-BOOK_TEMPLATE=book/minibook-templates/custom.html.jinja2
-DOCFORMAT=google
-
-# Agentic-specific variables
-DEFAULT_AI_MODEL=gpt-4.1
diff --git a/.rhiza/assets/rhiza-logo.svg b/.rhiza/assets/rhiza-logo.svg
new file mode 100644
index 00000000..ff1c9f57
--- /dev/null
+++ b/.rhiza/assets/rhiza-logo.svg
@@ -0,0 +1,81 @@
+<?xml version="1.0" encoding="UTF-8"?>
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diff --git a/.rhiza/make.d/01-custom-env.mk b/.rhiza/make.d/01-custom-env.mk
deleted file mode 100644
index 69c34c6f..00000000
--- a/.rhiza/make.d/01-custom-env.mk
+++ /dev/null
@@ -1,9 +0,0 @@
-## .rhiza/make.d/01-custom-env.mk - Custom Environment Configuration
-# This file example shows how to set variables for the project.
-
-# Custom variables for this repository
-PROJECT_NAME_EXTRA := Rhiza Platform
-LOG_LEVEL ?= INFO
-
-# Overriding core variables (be careful)
-# VENV := .venv_custom
diff --git a/.rhiza/make.d/10-custom-task.mk b/.rhiza/make.d/10-custom-task.mk
deleted file mode 100644
index 7c0ae036..00000000
--- a/.rhiza/make.d/10-custom-task.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-## .rhiza/make.d/10-custom-task.mk - Custom Repository Tasks
-# This file example shows how to add new targets.
-
-.PHONY: hello-rhiza
-
-##@ Custom Tasks
-hello-rhiza: ## a custom greeting task
-	@printf "${GREEN}[INFO] Hello from the customised Rhiza project!${RESET}\n"
-
-# Adding logic to existing hooks
-post-install:: ## run custom logic after core install
-	@printf "${BLUE}[INFO] Running custom post-install steps...${RESET}\n"
diff --git a/.rhiza/make.d/book.mk b/.rhiza/make.d/book.mk
new file mode 100644
index 00000000..28c77f60
--- /dev/null
+++ b/.rhiza/make.d/book.mk
@@ -0,0 +1,99 @@
+## book.mk - Book-building targets (MkDocs-based)
+
+.PHONY: book mkdocs-build test benchmark stress hypothesis-test _book-reports _book-notebooks mkdocs-serve mkdocs
+
+# No-op stubs — overridden by test.mk / bench.mk when present
+test:: ; @:
+benchmark:: ; @:
+stress:: ; @:
+hypothesis-test:: ; @:
+
+BOOK_OUTPUT ?= _book
+
+# Additional uvx --with packages to inject into mkdocs build and serve.
+# Projects can extend the package list without editing this template, e.g.:
+#   MKDOCS_EXTRA_PACKAGES = --with "mkdocs-graphviz"
+MKDOCS_EXTRA_PACKAGES ?=
+
+# Detect mkdocs config: prefer root-level, fall back to docs/mkdocs-base.yml
+_MKDOCS_CFG := $(if $(wildcard mkdocs.yml),mkdocs.yml,$(if $(wildcard docs/mkdocs-base.yml),docs/mkdocs-base.yml,))
+
+##@ Book
+
+_book-reports: test benchmark stress hypothesis-test
+	@mkdir -p docs/reports
+	@for src_dir in \
+	  "_tests/html-coverage:reports/coverage" \
+	  "_tests/html-report:reports/test-report" \
+	  "_tests/benchmarks:reports/benchmarks" \
+	  "_tests/stress:reports/stress" \
+	  "_tests/hypothesis:reports/hypothesis"; do \
+	  src=$${src_dir%%:*}; dest=docs/$${src_dir#*:}; \
+	  if [ -d "$$src" ] && [ -n "$$(ls -A "$$src" 2>/dev/null)" ]; then \
+	    printf "${BLUE}[INFO] Copying $$src -> $$dest${RESET}\n"; \
+	    mkdir -p "$$dest"; cp -r "$$src/." "$$dest/"; \
+	  else \
+	    printf "${YELLOW}[WARN] $$src not found, skipping${RESET}\n"; \
+	  fi; \
+	done
+	@printf "# Reports\n\n" > docs/reports.md
+	@[ -f "docs/reports/test-report/report.html" ] && echo "- [Test Report](reports/test-report/report.html)"       >> docs/reports.md || true
+	@[ -f "docs/reports/hypothesis/report.html" ]  && echo "- [Hypothesis Report](reports/hypothesis/report.html)" >> docs/reports.md || true
+	@[ -f "docs/reports/benchmarks/report.html" ]  && echo "- [Benchmarks](reports/benchmarks/report.html)"        >> docs/reports.md || true
+	@[ -f "docs/reports/stress/report.html" ]      && echo "- [Stress Report](reports/stress/report.html)"          >> docs/reports.md || true
+	@[ -f "docs/reports/coverage/index.html" ]     && echo "- [Coverage Report](reports/coverage/index.html)"      >> docs/reports.md || true
+
+_book-notebooks:
+	@if [ -d "$(MARIMO_FOLDER)" ]; then \
+	  for nb in $(MARIMO_FOLDER)/*.py; do \
+	    name=$$(basename "$$nb" .py); \
+	    printf "${BLUE}[INFO] Exporting $$nb${RESET}\n"; \
+	    abs_output="$$(pwd)/docs/notebooks/$$name.html"; \
+	    mkdir -p docs/notebooks; \
+	    (cd "$$(dirname "$$nb")" && ${UV_BIN} run marimo export html --sandbox "$$(basename "$$nb")" -o "$$abs_output"); \
+	  done; \
+	  printf "# Marimo Notebooks\n\n" > docs/notebooks.md; \
+	  for html in docs/notebooks/*.html; do \
+	    name=$$(basename "$$html" .html); \
+	    echo "- [$$name]($$name.html)" >> docs/notebooks.md; \
+	  done; \
+	fi
+
+book:: _book-reports _book-notebooks ## compile the companion book via MkDocs
+	@if [ -n "$(_MKDOCS_CFG)" ]; then \
+	  rm -rf "$(BOOK_OUTPUT)"; \
+	  ${UVX_BIN} --with "mkdocs-material<10.0" --with "pymdown-extensions>=10.0" --with "mkdocs<2.0" $(MKDOCS_EXTRA_PACKAGES) mkdocs build \
+	    -f "$(_MKDOCS_CFG)" \
+	    -d "$$(pwd)/$(BOOK_OUTPUT)"; \
+	else \
+	  printf "${YELLOW}[WARN] No mkdocs config found, skipping MkDocs build${RESET}\n"; \
+	fi
+	@mkdir -p "$(BOOK_OUTPUT)"
+	@touch "$(BOOK_OUTPUT)/.nojekyll"
+	@printf "${GREEN}[SUCCESS] Book built at $(BOOK_OUTPUT)/${RESET}\n"
+	@tree $(BOOK_OUTPUT)
+
+mkdocs-build: install-uv ## build MkDocs documentation site
+	@if [ -n "$(_MKDOCS_CFG)" ]; then \
+	  rm -rf "$(BOOK_OUTPUT)"; \
+	  ${UVX_BIN} --with "mkdocs-material<10.0" --with "pymdown-extensions>=10.0" --with "mkdocs<2.0" $(MKDOCS_EXTRA_PACKAGES) mkdocs build \
+	    -f "$(_MKDOCS_CFG)" \
+	    -d "$$(pwd)/$(BOOK_OUTPUT)"; \
+	else \
+	  printf "${RED}[ERROR] No mkdocs config found${RESET}\n"; \
+	  exit 1; \
+	fi
+	@mkdir -p "$(BOOK_OUTPUT)"
+	@touch "$(BOOK_OUTPUT)/.nojekyll"
+	@printf "${GREEN}[SUCCESS] Docs built at $(BOOK_OUTPUT)/${RESET}\n"
+
+mkdocs-serve: install-uv ## serve MkDocs site with live reload
+	@if [ -n "$(_MKDOCS_CFG)" ]; then \
+	  ${UVX_BIN} --with "mkdocs-material<10.0" --with "pymdown-extensions>=10.0" --with "mkdocs<2.0" $(MKDOCS_EXTRA_PACKAGES) mkdocs serve \
+	    -f "$(_MKDOCS_CFG)"; \
+	else \
+	  printf "${RED}[ERROR] No mkdocs config found${RESET}\n"; \
+	  exit 1; \
+	fi
+
+mkdocs: mkdocs-serve ## alias for mkdocs-serve
diff --git a/.rhiza/make.d/marimo.mk b/.rhiza/make.d/marimo.mk
new file mode 100644
index 00000000..36ae74ca
--- /dev/null
+++ b/.rhiza/make.d/marimo.mk
@@ -0,0 +1,42 @@
+## Makefile.marimo - Marimo notebook targets
+# This file is included by the main Makefile
+
+# Declare phony targets (they don't produce files)
+.PHONY: marimo-validate marimo
+
+##@ Marimo Notebooks
+marimo-validate: install ## validate all Marimo notebooks can run
+	@printf "${BLUE}[INFO] Validating all notebooks in ${MARIMO_FOLDER}...${RESET}\n"
+	@if [ ! -d "${MARIMO_FOLDER}" ]; then \
+	  printf "${YELLOW}[WARN] Directory '${MARIMO_FOLDER}' does not exist. Skipping validation.${RESET}\n"; \
+	else \
+	  failed=0; \
+	  for notebook in ${MARIMO_FOLDER}/*.py; do \
+	    if [ -f "$$notebook" ]; then \
+	      notebook_name=$$(basename "$$notebook"); \
+	      notebook_stem=$$(basename "$$notebook" .py); \
+	      artefact_folder="results/$$notebook_stem"; \
+	      mkdir -p "$$artefact_folder"; \
+	      printf "${BLUE}[INFO] Validating $$notebook_name (artefacts → $$artefact_folder)...${RESET}\n"; \
+	      if NOTEBOOK_OUTPUT_FOLDER="$$artefact_folder" ${UV_BIN} run "$$notebook" > /dev/null 2>&1; then \
+	        printf "${GREEN}[SUCCESS] $$notebook_name is valid${RESET}\n"; \
+	      else \
+	        printf "${RED}[ERROR] $$notebook_name failed validation${RESET}\n"; \
+	        failed=$$((failed + 1)); \
+	      fi; \
+	    fi; \
+	  done; \
+	  if [ $$failed -eq 0 ]; then \
+	    printf "${GREEN}[SUCCESS] All notebooks validated successfully${RESET}\n"; \
+	  else \
+	    printf "${RED}[ERROR] $$failed notebook(s) failed validation${RESET}\n"; \
+	    exit 1; \
+	  fi; \
+	fi
+
+marimo: install ## fire up Marimo server
+	@if [ ! -d "${MARIMO_FOLDER}" ]; then \
+	  printf " ${YELLOW}[WARN] Marimo folder '${MARIMO_FOLDER}' not found, skipping start${RESET}\n"; \
+	else \
+	  ${UV_BIN} run --no-project --with marimo --directory "${MARIMO_FOLDER}" marimo edit --no-token --headless; \
+	fi
diff --git a/.rhiza/make.d/quality.mk b/.rhiza/make.d/quality.mk
new file mode 100644
index 00000000..32007f33
--- /dev/null
+++ b/.rhiza/make.d/quality.mk
@@ -0,0 +1,51 @@
+## .rhiza/make.d/quality.mk - Quality and Formatting
+# This file provides targets for code quality checks, linting, and formatting.
+
+# Configurable list of licenses that fail the compliance scan (semicolon-separated)
+LICENSE_FAIL_ON ?= GPL;LGPL;AGPL
+
+# Declare phony targets (they don't produce files)
+.PHONY: all deptry fmt license todos suppression-audit
+
+##@ Quality and Formatting
+all: fmt deptry test docs-coverage security license typecheck rhiza-test ## run all CI targets locally
+
+deptry: install-uv ## Run deptry
+	@if [ -d ${SOURCE_FOLDER} ]; then \
+		$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${SOURCE_FOLDER}; \
+	fi
+
+	@if [ -d ${MARIMO_FOLDER} ]; then \
+		if [ -d ${SOURCE_FOLDER} ]; then \
+			$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${MARIMO_FOLDER} ${SOURCE_FOLDER} --ignore DEP004; \
+		else \
+		  	$(UVX_BIN) -p ${PYTHON_VERSION} deptry ${MARIMO_FOLDER} --ignore DEP004; \
+		fi \
+	fi
+
+fmt: install-uv ## check the pre-commit hooks and the linting
+	@${UVX_BIN} -p ${PYTHON_VERSION} pre-commit run --all-files
+
+todos: ## search and report all TODO/FIXME/HACK comments in the codebase
+	@printf "${BLUE}[INFO] Searching for TODO, FIXME, and HACK comments...${RESET}\n"
+	@printf "${BOLD}Found the following items:${RESET}\n\n"
+	@find . -type f \( -name "*.py" -o -name "*.mk" -o -name "*.sh" -o -name "*.md" -o -name "*.yml" -o -name "*.yaml" \) \
+		-not -path "./.venv/*" \
+		-not -path "./.git/*" \
+		-not -path "./node_modules/*" \
+		-not -path "./.tox/*" \
+		-not -path "./build/*" \
+		-not -path "./dist/*" \
+		-print0 | xargs -0 grep -nHE "(TODO|FIXME|HACK):" 2>/dev/null | \
+		grep -v "make todos" | \
+		awk -F: '{ printf "${YELLOW}%s${RESET}:${GREEN}%s${RESET}: %s\n", $$1, $$2, substr($$0, index($$0,$$3)) }' || \
+		printf "${GREEN}[SUCCESS] No TODO/FIXME/HACK comments found!${RESET}\n"
+	@printf "\n${BLUE}[INFO] Search complete.${RESET}\n"
+
+suppression-audit: ## scan codebase for inline suppressions and report (grade, detail, histogram)
+	@printf "${BLUE}[INFO] Running suppression audit...${RESET}\n"
+	@${UV_BIN} run python .rhiza/utils/suppression_audit.py
+
+license: install ## run license compliance scan (fail on GPL, LGPL, AGPL)
+	@printf "${BLUE}[INFO] Running license compliance scan...${RESET}\n"
+	@${UV_BIN} run --with pip-licenses pip-licenses --fail-on="${LICENSE_FAIL_ON}"
diff --git a/.rhiza/make.d/releasing.mk b/.rhiza/make.d/releasing.mk
new file mode 100644
index 00000000..fc6d57a6
--- /dev/null
+++ b/.rhiza/make.d/releasing.mk
@@ -0,0 +1,50 @@
+## .rhiza/make.d/releasing.mk - Releasing and Versioning
+# This file provides targets for version bumping and release management.
+
+# Declare phony targets (they don't produce files)
+.PHONY: bump release publish release-status pre-bump post-bump pre-release post-release
+
+# Hook targets (double-colon rules allow multiple definitions)
+pre-bump:: ; @:
+post-bump:: ; @:
+pre-release:: ; @:
+post-release:: ; @:
+
+# DRY_RUN support: pass DRY_RUN=1 to preview changes without applying them
+_DRY_RUN_FLAG := $(if $(DRY_RUN),--dry-run,)
+_VERSION=0.3.3
+
+##@ Releasing and Versioning
+bump: pre-bump ## bump version of the project (supports DRY_RUN=1)
+	@if [ -f "pyproject.toml" ]; then \
+		$(MAKE) install; \
+		PATH="$(abspath ${VENV})/bin:$$PATH" ${UVX_BIN} "rhiza-tools>=$(_VERSION)" bump $(_DRY_RUN_FLAG); \
+		if [ -z "$(DRY_RUN)" ]; then \
+			printf "${BLUE}[INFO] Checking uv.lock file...${RESET}\n"; \
+			${UV_BIN} lock; \
+		fi; \
+	else \
+		printf "${YELLOW}[WARN] No pyproject.toml found, skipping bump${RESET}\n"; \
+	fi
+	@$(MAKE) post-bump
+
+release: pre-release install-uv ## create tag and push to remote repository triggering release workflow (supports DRY_RUN=1)
+	${UVX_BIN} "rhiza-tools>=$(_VERSION)" release $(_DRY_RUN_FLAG);
+	@$(MAKE) post-release
+
+publish: pre-release install-uv ## bump version, create tag and push in one step (supports DRY_RUN=1)
+	${UVX_BIN} "rhiza-tools>=$(_VERSION)" release --with-bump $(_DRY_RUN_FLAG);
+	@$(MAKE) post-release
+
+release-status: ## show release workflow status and latest release information
+ifeq ($(FORGE_TYPE),github)
+	@{ $(MAKE) --no-print-directory workflow-status; printf "\n"; $(MAKE) --no-print-directory latest-release; } 2>&1 | $${PAGER:-less -R}
+else ifeq ($(FORGE_TYPE),gitlab)
+	@printf "${YELLOW}[WARN] GitLab detected — release-status is not yet supported for GitLab repositories.${RESET}\n"
+	@printf "${BLUE}[INFO] Please check your pipeline status in the GitLab UI.${RESET}\n"
+else
+	@printf "${RED}[ERROR] Could not detect forge type (.github/workflows/ or .gitlab-ci.yml not found)${RESET}\n"
+endif
+
+
+
diff --git a/.rhiza/requirements/README.md b/.rhiza/requirements/README.md
index 4feff9a7..5c7a818e 100644
--- a/.rhiza/requirements/README.md
+++ b/.rhiza/requirements/README.md
@@ -4,10 +4,10 @@ This folder contains the development dependencies for the Rhiza project, organiz
 
 ## Files
 
-- **tests.txt** - Testing dependencies (pytest, pytest-cov, pytest-html)
+- **tests.txt** - Testing dependencies (pytest, pytest-cov, pytest-html, pytest-mock, PyYAML, defusedxml, hypothesis, pytest-benchmark, pygal)
 - **marimo.txt** - Marimo notebook dependencies
-- **docs.txt** - Documentation generation dependencies (pdoc)
-- **tools.txt** - Development tools (pre-commit, python-dotenv)
+- **docs.txt** - Documentation generation dependencies (pdoc, interrogate, mkdocs, mkdocs-material, mkdocstrings)
+- **tools.txt** - Development tools (pre-commit, python-dotenv, typer, ty)
 
 ## Usage
 
diff --git a/.rhiza/requirements/docs.txt b/.rhiza/requirements/docs.txt
index 7d12b67f..1b9d3921 100644
--- a/.rhiza/requirements/docs.txt
+++ b/.rhiza/requirements/docs.txt
@@ -1,3 +1,5 @@
 # Documentation dependencies for rhiza
-pdoc>=16.0.0
 interrogate>=1.7.0
+mkdocs>=1.6.0
+mkdocs-material>=9.5.0
+mkdocstrings[python]>=0.25.0
diff --git a/.rhiza/requirements/tests.txt b/.rhiza/requirements/tests.txt
deleted file mode 100644
index fe03710f..00000000
--- a/.rhiza/requirements/tests.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-# Test dependencies for rhiza
-pytest>=8.0
-pytest-cov>=6.0
-pytest-html>=4.0
-pytest-mock>=3.0
-
-# For property-based testing
-hypothesis>=6.150.0
-
-# For benchmarks
-pytest-benchmark>=5.2.3
-pygal>=3.1.0
diff --git a/.rhiza/requirements/tools.txt b/.rhiza/requirements/tools.txt
index cb101c4f..262ffc01 100644
--- a/.rhiza/requirements/tools.txt
+++ b/.rhiza/requirements/tools.txt
@@ -1,6 +1,7 @@
 # Development tool dependencies for rhiza
 pre-commit==4.5.1
 python-dotenv==1.2.1
+
 # for now needed until rhiza-tools is finished
 typer==0.21.1
-mypy==1.19.1
+ty==0.0.18
diff --git a/.rhiza/scripts/check_workflow_names.py b/.rhiza/scripts/check_workflow_names.py
deleted file mode 100644
index e4a838d1..00000000
--- a/.rhiza/scripts/check_workflow_names.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/env python3
-"""Script to ensure GitHub Actions workflows have the (RHIZA) prefix."""
-
-import sys
-
-import yaml
-
-
-def check_file(filepath):
-    """Check if the workflow file has the correct name prefix and update if needed.
-
-    Args:
-        filepath: Path to the workflow file.
-
-    Returns:
-        bool: True if file is correct, False if it was updated or has errors.
-    """
-    with open(filepath) as f:
-        try:
-            content = yaml.safe_load(f)
-        except yaml.YAMLError as exc:
-            print(f"Error parsing YAML {filepath}: {exc}")
-            return False
-
-    if not isinstance(content, dict):
-        # Empty file or not a dict
-        return True
-
-    name = content.get("name")
-    if not name:
-        print(f"Error: {filepath} missing 'name' field.")
-        return False
-
-    if not name.startswith("(RHIZA) "):
-        print(f"Updating {filepath}: name '{name}' -> '(RHIZA) {name}'")
-
-        # Read file lines to perform replacement while preserving comments
-        with open(filepath) as f_read:
-            lines = f_read.readlines()
-
-        with open(filepath, "w") as f_write:
-            replaced = False
-            for line in lines:
-                # Replace only the top-level name field (assumes it starts at beginning of line)
-                if not replaced and line.startswith("name:"):
-                    # Check if this line corresponds to the extracted name.
-                    # Simple check: does it contain reasonable parts of the name?
-                    # Or just blinding replace top-level name:
-                    # We'll use quotes to be safe
-                    f_write.write(f'name: "(RHIZA) {name}"\n')
-                    replaced = True
-                else:
-                    f_write.write(line)
-
-        return False  # Fail so pre-commit knows files were modified
-
-    return True
-
-
-def main():
-    """Execute the script."""
-    files = sys.argv[1:]
-    failed = False
-    for f in files:
-        if not check_file(f):
-            failed = True
-
-    if failed:
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/.rhiza/scripts/release.sh b/.rhiza/scripts/release.sh
deleted file mode 100755
index 6ba0f218..00000000
--- a/.rhiza/scripts/release.sh
+++ /dev/null
@@ -1,276 +0,0 @@
-#!/bin/sh
-# Release script
-# - Creates a git tag based on the current version in pyproject.toml
-# - Pushes the tag to remote to trigger the release workflow
-# - Performs checks (branch, upstream status, clean working tree)
-#
-# This script is POSIX-sh compatible and follows the style of other scripts
-# in this repository. It uses uv to read the current version.
-
-set -eu
-
-UV_BIN=${UV_BIN:-./bin/uv}
-DRY_RUN=""
-
-BLUE="\033[36m"
-RED="\033[31m"
-GREEN="\033[32m"
-YELLOW="\033[33m"
-RESET="\033[0m"
-
-# Parse command-line arguments
-show_usage() {
-  printf "Usage: %s [OPTIONS]\n\n" "$0"
-  printf "Description:\n"
-  printf "  Create tag and push to remote (with prompts)\n\n"
-  printf "Options:\n"
-  printf "  -n, --dry-run  Show what would be done without making changes\n"
-  printf "  -h, --help     Show this help message\n\n"
-  printf "Examples:\n"
-  printf "  %s                                      (create tag and push with prompts)\n" "$0"
-  printf "  %s --dry-run                            (simulate release without changes)\n" "$0"
-}
-
-while [ $# -gt 0 ]; do
-  case "$1" in
-    -n|--dry-run)
-      DRY_RUN="true"
-      shift
-      ;;
-    -h|--help)
-      show_usage
-      exit 0
-      ;;
-    -*)
-      printf "%b[ERROR] Unknown option: %s%b\n" "$RED" "$1" "$RESET"
-      show_usage
-      exit 1
-      ;;
-    *)
-      printf "%b[ERROR] Unknown argument: %s%b\n" "$RED" "$1" "$RESET"
-      show_usage
-      exit 1
-      ;;
-  esac
-done
-
-# Check if pyproject.toml exists
-if [ ! -f "pyproject.toml" ]; then
-  printf "%b[ERROR] pyproject.toml not found in current directory%b\n" "$RED" "$RESET"
-  exit 1
-fi
-
-# Check if uv is available
-if [ ! -x "$UV_BIN" ]; then
-  printf "%b[ERROR] uv not found at %s. Run 'make install-uv' first.%b\n" "$RED" "$UV_BIN" "$RESET"
-  exit 1
-fi
-
-# Helper function to prompt user to continue
-# In dry-run mode, automatically continues without prompting
-prompt_continue() {
-  _pc_message="$1"
-  if [ -n "$DRY_RUN" ]; then
-    printf "\n%b[DRY-RUN] %s Would prompt to continue%b\n" "$YELLOW" "$_pc_message" "$RESET"
-    return 0
-  fi
-  printf "\n%b[PROMPT] %s Continue? [y/N] %b" "$YELLOW" "$_pc_message" "$RESET"
-  read -r _pc_answer
-  case "$_pc_answer" in
-    [Yy]*)
-      return 0
-      ;;
-    *)
-      printf "%b[INFO] Aborted by user%b\n" "$YELLOW" "$RESET"
-      exit 0
-      ;;
-  esac
-}
-
-# Helper function to prompt user for yes/no
-# In dry-run mode, automatically returns yes
-prompt_yes_no() {
-  _pyn_message="$1"
-  if [ -n "$DRY_RUN" ]; then
-    printf "\n%b[DRY-RUN] %s Would prompt yes/no%b\n" "$YELLOW" "$_pyn_message" "$RESET"
-    return 0
-  fi
-  printf "\n%b[PROMPT] %s [y/N] %b" "$YELLOW" "$_pyn_message" "$RESET"
-  read -r _pyn_answer
-  case "$_pyn_answer" in
-    [Yy]*)
-      return 0
-      ;;
-    *)
-      return 1
-      ;;
-  esac
-}
-
-# Function: Release - create tag and push (with prompts)
-do_release() {
-  # Get the current version from pyproject.toml
-  CURRENT_VERSION=$("$UV_BIN" version --short 2>/dev/null)
-  if [ -z "$CURRENT_VERSION" ]; then
-    printf "%b[ERROR] Could not determine version from pyproject.toml%b\n" "$RED" "$RESET"
-    exit 1
-  fi
-
-  TAG="v$CURRENT_VERSION"
-
-  # Get current branch
-  CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
-  if [ -z "$CURRENT_BRANCH" ]; then
-    printf "%b[ERROR] Could not determine current branch%b\n" "$RED" "$RESET"
-    exit 1
-  fi
-
-  # Determine default branch
-  DEFAULT_BRANCH=$(git remote show origin | grep 'HEAD branch' | cut -d' ' -f5)
-  if [ -z "$DEFAULT_BRANCH" ]; then
-    printf "%b[ERROR] Could not determine default branch from remote%b\n" "$RED" "$RESET"
-    exit 1
-  fi
-
-  # Warn if not on default branch
-  if [ "$CURRENT_BRANCH" != "$DEFAULT_BRANCH" ]; then
-    printf "%b[WARN] You are on branch '%s' but the default branch is '%s'%b\n" "$YELLOW" "$CURRENT_BRANCH" "$DEFAULT_BRANCH" "$RESET"
-    printf "%b[WARN] Releases are typically created from the default branch.%b\n" "$YELLOW" "$RESET"
-    prompt_continue "Proceed with release from '$CURRENT_BRANCH'?"
-  fi
-
-  printf "%b[INFO] Current version: %s%b\n" "$BLUE" "$CURRENT_VERSION" "$RESET"
-  printf "%b[INFO] Tag to create: %s%b\n" "$BLUE" "$TAG" "$RESET"
-
-  # Check if there are uncommitted changes
-  if [ -n "$(git status --porcelain)" ]; then
-    printf "%b[ERROR] You have uncommitted changes:%b\n" "$RED" "$RESET"
-    git status --short
-    printf "\n%b[ERROR] Please commit or stash your changes before releasing.%b\n" "$RED" "$RESET"
-    exit 1
-  fi
-
-  # Check if branch is up-to-date with remote
-  # This prevents releasing from an out-of-sync branch which could miss commits or conflict
-  printf "%b[INFO] Checking remote status...%b\n" "$BLUE" "$RESET"
-  git fetch origin >/dev/null 2>&1
-  # Get the upstream tracking branch (e.g., origin/main)
-  UPSTREAM=$(git rev-parse --abbrev-ref --symbolic-full-name '@{u}' 2>/dev/null)
-  if [ -z "$UPSTREAM" ]; then
-    printf "%b[ERROR] No upstream branch configured for %s%b\n" "$RED" "$CURRENT_BRANCH" "$RESET"
-    exit 1
-  fi
-  
-  # Compare local, remote, and merge-base commits to determine sync status
-  # LOCAL: current commit on local branch
-  # REMOTE: current commit on remote tracking branch
-  # BASE: most recent common ancestor between local and remote
-  LOCAL=$(git rev-parse @)
-  REMOTE=$(git rev-parse "$UPSTREAM")
-  BASE=$(git merge-base @ "$UPSTREAM")
-  
-  # Use git revision comparison to detect branch status
-  if [ "$LOCAL" != "$REMOTE" ]; then
-    if [ "$LOCAL" = "$BASE" ]; then
-        # Local is behind remote (need to pull)
-        printf "%b[ERROR] Your branch is behind '%s'. Please pull changes.%b\n" "$RED" "$UPSTREAM" "$RESET"
-        exit 1
-    elif [ "$REMOTE" = "$BASE" ]; then
-        # Local is ahead of remote (need to push)
-        printf "%b[WARN] Your branch is ahead of '%s'.%b\n" "$YELLOW" "$UPSTREAM" "$RESET"
-        printf "Unpushed commits:\n"
-        git log --oneline --graph --decorate "$UPSTREAM..HEAD"
-        prompt_continue "Push changes to remote before releasing?"
-        if [ -n "$DRY_RUN" ]; then
-          printf "%b[DRY-RUN] Would run: git push origin %s%b\n" "$YELLOW" "$CURRENT_BRANCH" "$RESET"
-        else
-          git push origin "$CURRENT_BRANCH"
-        fi
-    else
-        # Branches have diverged (need to merge or rebase)
-        printf "%b[ERROR] Your branch has diverged from '%s'. Please reconcile.%b\n" "$RED" "$UPSTREAM" "$RESET"
-        exit 1
-    fi
-  fi
-
-  # Check if tag already exists locally
-  SKIP_TAG_CREATE=""
-  if git rev-parse "$TAG" >/dev/null 2>&1; then
-    printf "%b[WARN] Tag '%s' already exists locally%b\n" "$YELLOW" "$TAG" "$RESET"
-    prompt_continue "Tag exists. Skip tag creation and proceed to push?"
-    SKIP_TAG_CREATE="true"
-  fi
-
-  # Check if tag already exists on remote
-  if git ls-remote --exit-code --tags origin "refs/tags/$TAG" >/dev/null 2>&1; then
-    printf "%b[ERROR] Tag '%s' already exists on remote%b\n" "$RED" "$TAG" "$RESET"
-    printf "The release for version %s has already been published.\n" "$CURRENT_VERSION"
-    exit 1
-  fi
-
-  # Step 1: Create the tag (if it doesn't exist)
-  if [ -z "$SKIP_TAG_CREATE" ]; then
-    printf "\n%b=== Step 1: Create Tag ===%b\n" "$BLUE" "$RESET"
-    printf "Creating tag '%s' for version %s\n" "$TAG" "$CURRENT_VERSION"
-    prompt_continue ""
-    
-    # Check if GPG signing is configured for git commits/tags
-    # If user.signingkey is set or commit.gpgsign is true, create a signed tag
-    # Signed tags provide cryptographic verification of release authenticity
-    if git config --get user.signingkey >/dev/null 2>&1 || [ "$(git config --get commit.gpgsign)" = "true" ]; then
-      printf "%b[INFO] GPG signing is enabled. Creating signed tag.%b\n" "$BLUE" "$RESET"
-      if [ -n "$DRY_RUN" ]; then
-        printf "%b[DRY-RUN] Would run: git tag -s %s -m \"Release %s\"%b\n" "$YELLOW" "$TAG" "$TAG" "$RESET"
-      else
-        git tag -s "$TAG" -m "Release $TAG"
-      fi
-    else
-      printf "%b[INFO] GPG signing is not enabled. Creating unsigned tag.%b\n" "$BLUE" "$RESET"
-      if [ -n "$DRY_RUN" ]; then
-        printf "%b[DRY-RUN] Would run: git tag -a %s -m \"Release %s\"%b\n" "$YELLOW" "$TAG" "$TAG" "$RESET"
-      else
-        git tag -a "$TAG" -m "Release $TAG"
-      fi
-    fi
-    if [ -n "$DRY_RUN" ]; then
-      printf "%b[DRY-RUN] Tag '%s' would be created locally%b\n" "$YELLOW" "$TAG" "$RESET"
-    else
-      printf "%b[SUCCESS] Tag '%s' created locally%b\n" "$GREEN" "$TAG" "$RESET"
-    fi
-  fi
-
-  # Step 2: Push the tag to remote
-  printf "\n%b=== Step 2: Push Tag to Remote ===%b\n" "$BLUE" "$RESET"
-  printf "Pushing tag '%s' to origin will trigger the release workflow.\n" "$TAG"
-  
-  # Show what commits are in this tag compared to the last tag
-  # This helps users understand what changes are included in the release
-  LAST_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "")
-  if [ -n "$LAST_TAG" ] && [ "$LAST_TAG" != "$TAG" ]; then
-    # Count commits between last tag and current tag
-    COMMIT_COUNT=$(git rev-list "$LAST_TAG..$TAG" --count 2>/dev/null || echo "0")
-    printf "Commits since %s: %s\n" "$LAST_TAG" "$COMMIT_COUNT"
-  fi
-  
-  prompt_continue ""
-
-  # Push only the specific tag (not all tags) to trigger the release workflow
-  # Extract repository name from remote URL for constructing GitHub Actions link
-  # Converts git@github.com:user/repo.git or https://github.com/user/repo.git to user/repo
-  REPO_URL=$(git remote get-url origin | sed 's/.*github.com[:/]\(.*\)\.git/\1/')
-
-  if [ -n "$DRY_RUN" ]; then
-    printf "%b[DRY-RUN] Would run: git push origin refs/tags/%s%b\n" "$YELLOW" "$TAG" "$RESET"
-    printf "\n%b[DRY-RUN] Release tag %s would be pushed to remote%b\n" "$YELLOW" "$TAG" "$RESET"
-    printf "%b[DRY-RUN] This would trigger the release workflow%b\n" "$YELLOW" "$RESET"
-    printf "%b[INFO] Monitor progress at: https://github.com/%s/actions%b\n" "$BLUE" "$REPO_URL" "$RESET"
-  else
-    git push origin "refs/tags/$TAG"
-    printf "\n%b[SUCCESS] Release tag %s pushed to remote!%b\n" "$GREEN" "$TAG" "$RESET"
-    printf "%b[INFO] The release workflow will now be triggered automatically.%b\n" "$BLUE" "$RESET"
-    printf "%b[INFO] Monitor progress at: https://github.com/%s/actions%b\n" "$BLUE" "$REPO_URL" "$RESET"
-  fi
-}
-
-# Main execution logic
-do_release
diff --git a/.rhiza/template.lock b/.rhiza/template.lock
new file mode 100644
index 00000000..6e08fe14
--- /dev/null
+++ b/.rhiza/template.lock
@@ -0,0 +1,64 @@
+sha: dccf929ce3bcbaf01ddf1240ac16354e0cf76bb1
+repo: jebel-quant/rhiza
+host: github
+ref: v0.9.5
+include: []
+exclude:
+- .rhiza/docs/
+- .rhiza/make.d/agentic.mk
+- .rhiza/make.d/gh-aw.mk
+- .rhiza/make.d/github.mk
+- .rhiza/make.d/custom-env.mk
+- .rhiza/make.d/custom-task.mk
+- .rhiza/make.d/README.md
+- .github/agents/
+- docs/adr
+templates:
+- github
+- marimo
+files:
+- .editorconfig
+- .github/DISCUSSION_TEMPLATE/q-and-a.yml
+- .github/ISSUE_TEMPLATE/bug_report.yml
+- .github/ISSUE_TEMPLATE/feature_request.yml
+- .github/actions/configure-git-auth/README.md
+- .github/actions/configure-git-auth/action.yml
+- .github/copilot-instructions.md
+- .github/dependabot.yml
+- .github/hooks/hooks.json
+- .github/hooks/session-end.sh
+- .github/hooks/session-start.sh
+- .github/secret_scanning.yml
+- .github/semgrep.yml
+- .github/workflows/copilot-setup-steps.yml
+- .github/workflows/rhiza_book.yml
+- .github/workflows/rhiza_marimo.yml
+- .github/workflows/rhiza_release.yml
+- .github/workflows/rhiza_sync.yml
+- .github/workflows/rhiza_weekly.yml
+- .gitignore
+- .pre-commit-config.yaml
+- .python-version
+- .rhiza/.cfg.toml
+- .rhiza/.env
+- .rhiza/.gitignore
+- .rhiza/.rhiza-version
+- .rhiza/assets/rhiza-logo.svg
+- .rhiza/make.d/book.mk
+- .rhiza/make.d/bootstrap.mk
+- .rhiza/make.d/marimo.mk
+- .rhiza/make.d/quality.mk
+- .rhiza/make.d/releasing.mk
+- .rhiza/requirements/README.md
+- .rhiza/requirements/docs.txt
+- .rhiza/requirements/marimo.txt
+- .rhiza/requirements/tools.txt
+- .rhiza/rhiza.mk
+- Makefile
+- docs/assets/rhiza-logo.svg
+- docs/development/MARIMO.md
+- docs/index.md
+- docs/mkdocs-base.yml
+- ruff.toml
+synced_at: '2026-04-16T02:49:17Z'
+strategy: merge
diff --git a/.rhiza/utils/version_matrix.py b/.rhiza/utils/version_matrix.py
deleted file mode 100755
index 08ef655a..00000000
--- a/.rhiza/utils/version_matrix.py
+++ /dev/null
@@ -1,152 +0,0 @@
-#!/usr/bin/env python3
-"""Emit the list of supported Python versions from pyproject.toml.
-
-This helper is used in GitHub Actions to compute the test matrix.
-"""
-
-import json
-import re
-import tomllib
-from pathlib import Path
-
-PYPROJECT = Path(__file__).resolve().parents[2] / "pyproject.toml"
-CANDIDATES = ["3.11", "3.12", "3.13", "3.14"]  # extend as needed
-
-
-class RhizaError(Exception):
-    """Base exception for Rhiza-related errors."""
-
-
-class VersionSpecifierError(RhizaError):
-    """Raised when a version string or specifier is invalid."""
-
-
-class PyProjectError(RhizaError):
-    """Raised when there are issues with pyproject.toml configuration."""
-
-
-def parse_version(v: str) -> tuple[int, ...]:
-    """Parse a version string into a tuple of integers.
-
-    This is intentionally simple and only supports numeric components.
-    If a component contains non-numeric suffixes (e.g. '3.11.0rc1'),
-    the leading numeric portion will be used (e.g. '0rc1' -> 0). If a
-    component has no leading digits at all, a VersionSpecifierError is raised.
-
-    Args:
-        v: Version string to parse (e.g., "3.11", "3.11.0rc1").
-
-    Returns:
-        Tuple of integers representing the version.
-
-    Raises:
-        VersionSpecifierError: If a version component has no numeric prefix.
-    """
-    parts: list[int] = []
-    for part in v.split("."):
-        match = re.match(r"\d+", part)
-        if not match:
-            msg = f"Invalid version component {part!r} in version {v!r}; expected a numeric prefix."
-            raise VersionSpecifierError(msg)
-        parts.append(int(match.group(0)))
-    return tuple(parts)
-
-
-def _check_operator(version_tuple: tuple[int, ...], op: str, spec_v_tuple: tuple[int, ...]) -> bool:
-    """Check if a version tuple satisfies an operator constraint."""
-    operators = {
-        ">=": lambda v, s: v >= s,
-        "<=": lambda v, s: v <= s,
-        ">": lambda v, s: v > s,
-        "<": lambda v, s: v < s,
-        "==": lambda v, s: v == s,
-        "!=": lambda v, s: v != s,
-    }
-    return operators[op](version_tuple, spec_v_tuple)
-
-
-def satisfies(version: str, specifier: str) -> bool:
-    """Check if a version satisfies a comma-separated list of specifiers.
-
-    This is a simplified version of packaging.specifiers.SpecifierSet.
-    Supported operators: >=, <=, >, <, ==, !=
-
-    Args:
-        version: Version string to check (e.g., "3.11").
-        specifier: Comma-separated specifier string (e.g., ">=3.11,<3.14").
-
-    Returns:
-        True if the version satisfies all specifiers, False otherwise.
-
-    Raises:
-        VersionSpecifierError: If the specifier format is invalid.
-    """
-    version_tuple = parse_version(version)
-
-    # Split by comma for multiple constraints
-    for spec in specifier.split(","):
-        spec = spec.strip()
-        # Match operator and version part
-        match = re.match(r"(>=|<=|>|<|==|!=)\s*([\d.]+)", spec)
-        if not match:
-            # If no operator, assume ==
-            if re.match(r"[\d.]+", spec):
-                if version_tuple != parse_version(spec):
-                    return False
-                continue
-            msg = f"Invalid specifier {spec!r}; expected format like '>=3.11' or '3.11'"
-            raise VersionSpecifierError(msg)
-
-        op, spec_v = match.groups()
-        spec_v_tuple = parse_version(spec_v)
-
-        if not _check_operator(version_tuple, op, spec_v_tuple):
-            return False
-
-    return True
-
-
-def supported_versions() -> list[str]:
-    """Return all supported Python versions declared in pyproject.toml.
-
-    Reads project.requires-python, evaluates candidate versions against the
-    specifier, and returns the subset that satisfy the constraint, in ascending order.
-
-    Returns:
-        list[str]: The supported versions (e.g., ["3.11", "3.12"]).
-
-    Raises:
-        PyProjectError: If requires-python is missing or no candidates match.
-    """
-    # Load pyproject.toml using the tomllib standard library (Python 3.11+)
-    with PYPROJECT.open("rb") as f:
-        data = tomllib.load(f)
-
-    # Extract the requires-python field from project metadata
-    # This specifies the Python version constraint (e.g., ">=3.11")
-    spec_str = data.get("project", {}).get("requires-python")
-    if not spec_str:
-        msg = "pyproject.toml: missing 'project.requires-python'"
-        raise PyProjectError(msg)
-
-    # Filter candidate versions to find which ones satisfy the constraint
-    versions: list[str] = []
-    for v in CANDIDATES:
-        if satisfies(v, spec_str):
-            versions.append(v)
-
-    if not versions:
-        msg = f"pyproject.toml: no supported Python versions match '{spec_str}'. Evaluated candidates: {CANDIDATES}"
-        raise PyProjectError(msg)
-
-    return versions
-
-
-if __name__ == "__main__":
-    # Check if pyproject.toml exists in the expected location
-    # If it exists, use it to determine supported versions
-    # Otherwise, fall back to returning all candidates (for edge cases)
-    if PYPROJECT.exists():
-        print(json.dumps(supported_versions()))
-    else:
-        print(json.dumps(CANDIDATES))
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
deleted file mode 100644
index 41f0e9c2..00000000
--- a/CODE_OF_CONDUCT.md
+++ /dev/null
@@ -1,27 +0,0 @@
-# Code of Conduct
-
-## Purpose
-
-This code of conduct outlines expectations for behaviour when participating in the project with the aim of fostering a constructive and professional engineering environment.
-
-## Expected Behaviour
-
-Participants are expected to:
-
-- Be respectful in communication and collaboration.
-- Focus on technical topics and project goals.
-- Accept constructive feedback gracefully and offer it in kind.
-- Assume good intentions from others and engage with a problem-solving mindset.
-- Use appropriate language and conduct in all community spaces.
-
-## Scope
-
-This Code of Conduct applies in all project spaces—online and offline—and also applies when individuals are representing the project in public spaces.
-
-## Enforcement
-
-Project maintainers are responsible for enforcing the code and may take proportionate corrective action in response to unexpected behaviour.
-
-## Attribution
-
-Adapted from the [Contributor Covenant](https://www.contributor-covenant.org), with modifications for brevity and neutrality.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 100644
index d8603155..00000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1,93 +0,0 @@
-# Contributing
-
-This document is a guide to contributing to the project.
-
-We welcome all contributions. You don't need to be an expert
-to help out.
-
-## Checklist
-
-Contributions are made through
-[pull requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests).
-Before sending a pull request, make sure you do the following:
-
-- Run `make fmt` to make sure your code adheres to our [coding style](#code-style)
-and all tests pass.
-- [Write unit tests](#writing-unit-tests) for new functionality added.
-
-## Building from source
-
-You'll need to build the project locally to start editing code.
-To install from source, clone the repository from GitHub, 
-navigate to its root, and run the following command:
-
-```bash
-make install
-```
-
-## Contributing code
-
-To contribute to the project, send us pull requests.
-For those new to contributing, check out GitHub's
-[guide](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests).
-
-Once you've made your pull request, a member of the
-development team will assign themselves to review it.
-You might have a few
-back-and-forths with your reviewer before it is accepted,
-which is completely normal.
-Your pull request will trigger continuous integration tests
-for many different
-Python versions and different platforms. If these tests start failing,
-please
-fix your code and send another commit, which will re-trigger the tests.
-
-If you'd like to add a new feature, please propose your
-change in a GitHub issue to make sure
-that your priorities align with ours.
-
-If you'd like to contribute code but don't know where to start,
-try one of the
-following:
-
-- Read the source and enhance the documentation,
-  or address TODOs
-- Browse the open issues,
-  and look for the issues tagged "help wanted".
-
-## Code style
-
-We use ruff to enforce our Python coding style.
-Before sending us a pull request, navigate to the project 
-root and run
-
-```bash
-make fmt
-```
-
-to make sure that your changes abide by our style conventions.
-Please fix any errors that are reported before sending
-the pull request.
-
-## Writing unit tests
-
-Most code changes will require new unit tests.
-Even bug fixes require unit tests,
-since the presence of bugs usually indicates insufficient tests.
-When adding tests, try to find a file in which your tests should belong;
-if you're testing a new feature, you might want to create a new test file.
-
-We use the popular Python [pytest](https://docs.pytest.org/en/) framework for our
-tests.
-
-## Running unit tests
-
-We use `pytest` to run our unit tests.
-To run all unit tests run the following command:
-
-```bash
-make test
-```
-
-Please make sure that your change doesn't cause any
-of the unit tests to fail.
diff --git a/Makefile b/Makefile
index 0a1aac7f..24239e6f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,8 +1,49 @@
 ## Makefile (repo-owned)
 # Keep this file small. It can be edited without breaking template sync.
 
+DOCFORMAT=google
+DEFAULT_AI_MODEL=claude-sonnet-4.5
+LOGO_FILE=.rhiza/assets/rhiza-logo.svg
+GH_AW_ENGINE ?= copilot  # Default AI engine for gh-aw workflows (copilot, claude, or codex)
+
 # Always include the Rhiza API (template-managed)
 include .rhiza/rhiza.mk
 
 # Optional: developer-local extensions (not committed)
 -include local.mk
+
+# Wire typecheck into make validate
+post-validate::
+	@$(MAKE) typecheck
+
+## Custom targets
+
+.PHONY: adr
+adr: install-gh-aw ## Create a new Architecture Decision Record (ADR) using AI assistance
+	@echo "Creating a new ADR..."
+	@echo "This will trigger the adr-create workflow."
+	@echo ""
+	@read -p "Enter ADR title (e.g., 'Use PostgreSQL for data storage'): " title; \
+	echo ""; \
+	read -p "Enter brief context (optional, press Enter to skip): " context; \
+	echo ""; \
+	if [ -z "$$title" ]; then \
+		echo "Error: Title is required"; \
+		exit 1; \
+	fi; \
+	if [ -z "$$context" ]; then \
+		gh workflow run adr-create.md -f title="$$title"; \
+	else \
+		gh workflow run adr-create.md -f title="$$title" -f context="$$context"; \
+	fi; \
+	echo ""; \
+	echo "✅ ADR creation workflow triggered!"; \
+	echo ""; \
+	echo "The workflow will:"; \
+	echo "  1. Generate the next ADR number"; \
+	echo "  2. Create a comprehensive ADR document"; \
+	echo "  3. Update the ADR index"; \
+	echo "  4. Open a pull request for review"; \
+	echo ""; \
+	echo "Check workflow status: gh run list --workflow=adr-create.md"; \
+	echo "View latest run: gh run view"
diff --git a/book/README.md b/book/README.md
deleted file mode 100644
index 81273af2..00000000
--- a/book/README.md
+++ /dev/null
@@ -1,67 +0,0 @@
-# Project Book and Documentation
-
-This directory contains the source and templates for generating the Rhiza companion book and API documentation.
-
-## Structure
-
-- `marimo/`: Interactive [Marimo](https://marimo.io/) notebooks that are included in the book.
-- `minibook-templates/`: Jinja2 templates for the minibook generation.
-- `pdoc-templates/`: Custom templates for [pdoc](https://pdoc.dev/) API documentation.
-- `book.mk`: Specialised Makefile for building the book and documentation.
-
-## Building the Book
-
-You can build the complete documentation book using the main project Makefile:
-
-```bash
-make book
-```
-
-This process involves:
-1. Exporting Marimo notebooks to HTML.
-2. Generating API documentation from the source code.
-3. Combining them into a cohesive "book" structure.
-
-## Documentation Customisation
-
-You can customise the look and feel of your documentation by providing your own templates.
-
-### API Documentation (pdoc)
-
-The `make docs` command checks for a directory at `book/pdoc-templates`. If found, it uses the templates within that directory to generate the API documentation.
-
-To customise the API docs:
-1. Create the directory: `mkdir -p book/pdoc-templates`
-2. Add your Jinja2 templates (e.g., `module.html.jinja2`) to this directory.
-
-See the [pdoc documentation](https://pdoc.dev/docs/pdoc.html#templates) for more details on templating.
-
-### Project Logo
-
-The documentation generation supports embedding a project logo in the sidebar.
-
-**Default Behavior:**
-By default, the build looks for `assets/rhiza-logo.svg`.
-
-**Customization:**
-You can change the logo by setting the `LOGO_FILE` variable in your project's `Makefile` or `local.mk`.
-
-```makefile
-# Example: Use a custom PNG logo
-LOGO_FILE := assets/my-company-logo.png
-```
-
-To disable the logo entirely, set the variable to an empty string:
-
-```makefile
-# Example: Disable logo
-LOGO_FILE :=
-```
-
-### Companion Book (minibook)
-
-The `make book` command checks for a template at `book/minibook-templates/custom.html.jinja2`. If found, it uses this template for the minibook generation.
-
-To customise the book:
-1. Create the directory: `mkdir -p book/minibook-templates`
-2. Create your custom template at `book/minibook-templates/custom.html.jinja2`.
diff --git a/book/book.mk b/book/book.mk
deleted file mode 100644
index 5c2fc17b..00000000
--- a/book/book.mk
+++ /dev/null
@@ -1,166 +0,0 @@
-## book.mk - Documentation and book-building targets
-# This file is included by the main Makefile.
-# It provides targets for generating API documentation (pdoc),
-# exporting Marimo notebooks to HTML (marimushka), and compiling
-# a companion book (minibook).
-
-# Declare phony targets (they don't produce files)
-.PHONY: docs marimushka book
-
-# Define a default no-op marimushka target that will be used
-# when book/marimo/marimo.mk doesn't exist or doesn't define marimushka
-marimushka:: install-uv
-	@if [ ! -d "book/marimo" ]; then \
-	  printf "${BLUE}[INFO] No Marimo directory found, creating placeholder${RESET}\n"; \
-	  mkdir -p "${MARIMUSHKA_OUTPUT}"; \
-	  printf '%s\n' '<html><head><title>Marimo Notebooks</title></head>' \
-	    '<body><h1>Marimo Notebooks</h1><p>No notebooks found.</p></body></html>' \
-	    > "${MARIMUSHKA_OUTPUT}/index.html"; \
-	fi
-
-# Default output directory for Marimushka (HTML exports of notebooks)
-MARIMUSHKA_OUTPUT ?= _marimushka
-
-# Logo file for pdoc (relative to project root).
-# 1. Defaults to the Rhiza logo if present.
-# 2. Can be overridden in Makefile or local.mk (e.g. LOGO_FILE := my-logo.png)
-# 3. If set to empty string, no logo will be used.
-LOGO_FILE ?= assets/rhiza-logo.svg
-
-# ----------------------------
-# Book sections (declarative)
-# ----------------------------
-# format:
-#   name | source index | book-relative index | source dir | book dir
-
-BOOK_SECTIONS := \
-  "API|_pdoc/index.html|pdoc/index.html|_pdoc|pdoc" \
-  "Coverage|_tests/html-coverage/index.html|tests/html-coverage/index.html|_tests/html-coverage|tests/html-coverage" \
-  "Test Report|_tests/html-report/report.html|tests/html-report/report.html|_tests/html-report|tests/html-report" \
-  "Notebooks|_marimushka/index.html|marimushka/index.html|_marimushka|marimushka"
-
-
-##@ Documentation
-
-# The 'docs' target generates API documentation using pdoc.
-# 1. Identifies Python packages within the source folder.
-# 2. Detects the docformat (google, numpy, or sphinx) from ruff.toml or defaults to google.
-# 3. Installs pdoc and generates HTML documentation in _pdoc.
-docs:: install ## create documentation with pdoc
-	# Clean up previous docs
-	rm -rf _pdoc;
-
-	@if [ -d "${SOURCE_FOLDER}" ]; then \
-	  PKGS=""; for d in "${SOURCE_FOLDER}"/*; do [ -d "$$d" ] && PKGS="$$PKGS $$(basename "$$d")"; done; \
-	  if [ -z "$$PKGS" ]; then \
-	    printf "${YELLOW}[WARN] No packages found under ${SOURCE_FOLDER}, skipping docs${RESET}\n"; \
-	  else \
-	    TEMPLATE_ARG=""; \
-	    if [ -d "${PDOC_TEMPLATE_DIR}" ]; then \
-	      TEMPLATE_ARG="-t ${PDOC_TEMPLATE_DIR}"; \
-	      printf "${BLUE}[INFO] Using pdoc templates from ${PDOC_TEMPLATE_DIR}${RESET}\n"; \
-	    fi; \
-	    DOCFORMAT="$(DOCFORMAT)"; \
-	    if [ -z "$$DOCFORMAT" ]; then \
-	      if [ -f "ruff.toml" ]; then \
-	        DOCFORMAT=$$(${UV_BIN} run python -c "import tomllib; print(tomllib.load(open('ruff.toml', 'rb')).get('lint', {}).get('pydocstyle', {}).get('convention', ''))"); \
-	      fi; \
-	      if [ -z "$$DOCFORMAT" ]; then \
-	        DOCFORMAT="google"; \
-	      fi; \
-	      printf "${BLUE}[INFO] Detected docformat: $$DOCFORMAT${RESET}\n"; \
-	    else \
-	      printf "${BLUE}[INFO] Using provided docformat: $$DOCFORMAT${RESET}\n"; \
-	    fi; \
-	    LOGO_ARG=""; \
-	    if [ -n "$(LOGO_FILE)" ]; then \
-	      if [ -f "$(LOGO_FILE)" ]; then \
-	        MIME=$$(file --mime-type -b "$(LOGO_FILE)"); \
-	        DATA=$$(base64 < "$(LOGO_FILE)" | tr -d '\n'); \
-	        LOGO_ARG="--logo data:$$MIME;base64,$$DATA"; \
-	        printf "${BLUE}[INFO] Embedding logo: $(LOGO_FILE)${RESET}\n"; \
-	      else \
-	        printf "${YELLOW}[WARN] Logo file $(LOGO_FILE) not found, skipping${RESET}\n"; \
-	      fi; \
-	    fi; \
-	    ${UV_BIN} pip install pdoc && \
-	    PYTHONPATH="${SOURCE_FOLDER}" ${UV_BIN} run pdoc --docformat $$DOCFORMAT --output-dir _pdoc $$TEMPLATE_ARG $$LOGO_ARG $$PKGS; \
-	  fi; \
-	else \
-	  printf "${YELLOW}[WARN] Source folder ${SOURCE_FOLDER} not found, skipping docs${RESET}\n"; \
-	fi
-
-# The 'book' target assembles the final documentation book.
-# 1. Aggregates API docs, coverage, test reports, and notebooks into _book.
-# 2. Generates links.json to define the book structure.
-# 3. Uses 'minibook' to compile the final HTML site.
-book:: install-uv ## compile the companion book
-	@printf "${BLUE}[INFO] Building combined documentation...${RESET}\n"
-
-	# Run docs but don't fail book if docs fail or are unavailable
-	@$(MAKE) docs || printf "${YELLOW}[WARN] Docs failed or unavailable, continuing with book generation${RESET}\n"
-
-	# Run marimushka but don't fail book if marimushka fails or is unavailable
-	@$(MAKE) marimushka || printf "${YELLOW}[WARN] Marimushka failed or unavailable, continuing with book generation${RESET}\n"
-
-	# Run tests but don't fail book if tests fail or are unavailable
-	@$(MAKE) test || printf "${YELLOW}[WARN] Tests failed or unavailable, continuing with book generation${RESET}\n"
-
-	@rm -rf _book && mkdir -p _book
-
-	@if [ -f "_tests/coverage.json" ]; then \
-	  printf "${BLUE}[INFO] Generating coverage badge JSON...${RESET}\n"; \
-	  mkdir -p _book/tests; \
-	  ${UV_BIN} run python -c "\
-import json; \
-data = json.load(open('_tests/coverage.json')); \
-pct = int(data['totals']['percent_covered']); \
-color = 'brightgreen' if pct >= 90 else 'green' if pct >= 80 else 'yellow' if pct >= 70 else 'orange' if pct >= 60 else 'red'; \
-badge = {'schemaVersion': 1, 'label': 'coverage', 'message': f'{pct}%', 'color': color}; \
-json.dump(badge, open('_book/tests/coverage-badge.json', 'w'))"; \
-	  printf "${BLUE}[INFO] Coverage badge JSON:${RESET}\n"; \
-	  cat _book/tests/coverage-badge.json; \
-	  printf "\n"; \
-	else \
-	  printf "${YELLOW}[WARN] No coverage.json found, skipping badge generation${RESET}\n"; \
-	fi
-
-	@printf "{\n" > _book/links.json
-	@first=1; \
-	for entry in $(BOOK_SECTIONS); do \
-	  name=$${entry%%|*}; \
-	  rest=$${entry#*|}; \
-	  src_index=$${rest%%|*}; rest=$${rest#*|}; \
-	  book_index=$${rest%%|*}; rest=$${rest#*|}; \
-	  src_dir=$${rest%%|*}; book_dir=$${rest#*|}; \
-	  if [ -f "$$src_index" ]; then \
-	    printf "${BLUE}[INFO] Adding $$name...${RESET}\n"; \
-	    mkdir -p "_book/$$book_dir"; \
-	    cp -r "$$src_dir/"* "_book/$$book_dir"; \
-	    if [ $$first -eq 0 ]; then \
-	      printf ",\n" >> _book/links.json; \
-	    fi; \
-	    printf "  \"%s\": \"./%s\"" "$$name" "$$book_index" >> _book/links.json; \
-	    first=0; \
-	  else \
-	    printf "${YELLOW}[WARN] Missing $$name, skipping${RESET}\n"; \
-	  fi; \
-	done; \
-	printf "\n}\n" >> _book/links.json
-
-	@printf "${BLUE}[INFO] Generated links.json:${RESET}\n"
-	@cat _book/links.json
-
-	@TEMPLATE_ARG=""; \
-	if [ -f "$(BOOK_TEMPLATE)" ]; then \
-	  TEMPLATE_ARG="--template $(BOOK_TEMPLATE)"; \
-	  printf "${BLUE}[INFO] Using book template $(BOOK_TEMPLATE)${RESET}\n"; \
-	fi; \
-	"$(UVX_BIN)" minibook \
-	  --title "$(BOOK_TITLE)" \
-	  --subtitle "$(BOOK_SUBTITLE)" \
-	  $$TEMPLATE_ARG \
-	  --links "$$(python3 -c 'import json;print(json.dumps(json.load(open("_book/links.json"))))')" \
-	  --output "_book"
-
-	@touch "_book/.nojekyll"
diff --git a/book/marimo/marimo.mk b/book/marimo/marimo.mk
deleted file mode 100644
index 25975735..00000000
--- a/book/marimo/marimo.mk
+++ /dev/null
@@ -1,67 +0,0 @@
-## Makefile.marimo - Marimo notebook targets
-# This file is included by the main Makefile
-
-# Declare phony targets (they don't produce files)
-.PHONY: marimo-validate marimo marimushka
-
-##@ Marimo Notebooks
-marimo-validate: install ## validate all Marimo notebooks can run
-	@printf "${BLUE}[INFO] Validating all notebooks in ${MARIMO_FOLDER}...${RESET}\n"
-	@if [ ! -d "${MARIMO_FOLDER}" ]; then \
-	  printf "${YELLOW}[WARN] Directory '${MARIMO_FOLDER}' does not exist. Skipping validation.${RESET}\n"; \
-	else \
-	  failed=0; \
-	  for notebook in ${MARIMO_FOLDER}/*.py; do \
-	    if [ -f "$$notebook" ]; then \
-	      notebook_name=$$(basename "$$notebook"); \
-	      printf "${BLUE}[INFO] Validating $$notebook_name...${RESET}\n"; \
-	      if ${UV_BIN} run "$$notebook" > /dev/null 2>&1; then \
-	        printf "${GREEN}[SUCCESS] $$notebook_name is valid${RESET}\n"; \
-	      else \
-	        printf "${RED}[ERROR] $$notebook_name failed validation${RESET}\n"; \
-	        failed=$$((failed + 1)); \
-	      fi; \
-	    fi; \
-	  done; \
-	  if [ $$failed -eq 0 ]; then \
-	    printf "${GREEN}[SUCCESS] All notebooks validated successfully${RESET}\n"; \
-	  else \
-	    printf "${RED}[ERROR] $$failed notebook(s) failed validation${RESET}\n"; \
-	    exit 1; \
-	  fi; \
-	fi
-
-marimo: install ## fire up Marimo server
-	@if [ ! -d "${MARIMO_FOLDER}" ]; then \
-	  printf " ${YELLOW}[WARN] Marimo folder '${MARIMO_FOLDER}' not found, skipping start${RESET}\n"; \
-	else \
-	  ${UV_BIN} run --with marimo marimo edit --no-token --headless "${MARIMO_FOLDER}"; \
-	fi
-
-# The 'marimushka' target exports Marimo notebooks (.py files) to static HTML.
-# 1. Detects notebooks in the MARIMO_FOLDER.
-# 2. Converts them using 'marimushka export'.
-# 3. Generates a placeholder index.html if no notebooks are found.
-marimushka:: install-uv ## export Marimo notebooks to HTML
-	# Clean up previous marimushka output
-	rm -rf "${MARIMUSHKA_OUTPUT}";
-
-	@printf "${BLUE}[INFO] Exporting notebooks from ${MARIMO_FOLDER}...${RESET}\n"
-	@if [ ! -d "${MARIMO_FOLDER}" ]; then \
-	  printf "${YELLOW}[WARN] Directory '${MARIMO_FOLDER}' does not exist. Skipping marimushka.${RESET}\n"; \
-	else \
-	  mkdir -p "${MARIMUSHKA_OUTPUT}"; \
-	  if ! ls "${MARIMO_FOLDER}"/*.py >/dev/null 2>&1; then \
-	    printf "${YELLOW}[WARN] No Python files found in '${MARIMO_FOLDER}'.${RESET}\n"; \
-	    printf '%s\n' '<html><head><title>Marimo Notebooks</title></head>' \
-	      '<body><h1>Marimo Notebooks</h1><p>No notebooks found.</p></body></html>' \
-	      > "${MARIMUSHKA_OUTPUT}/index.html"; \
-	  else \
-	    CURRENT_DIR=$$(pwd); \
-	    OUTPUT_DIR="$$CURRENT_DIR/${MARIMUSHKA_OUTPUT}"; \
-	    cd "${MARIMO_FOLDER}" && \
-	    UVX_DIR=$$(dirname "$$(command -v uvx || echo "${INSTALL_DIR}/uvx")") && \
-	    "${UVX_BIN}" "marimushka>=0.1.9" export --notebooks "." --output "$$OUTPUT_DIR" --bin-path "$$UVX_DIR" && \
-	    cd "$$CURRENT_DIR"; \
-	  fi; \
-	fi
diff --git a/book/marimo/notebooks/rhiza.py b/book/marimo/notebooks/rhiza.py
deleted file mode 100644
index 8167c6c9..00000000
--- a/book/marimo/notebooks/rhiza.py
+++ /dev/null
@@ -1,629 +0,0 @@
-"""Marimo Showcase Notebook - Demonstrating Key Features.
-
-This notebook showcases the most useful features of Marimo, including:
-- Interactive UI elements (sliders, dropdowns, text inputs)
-- Reactive programming (automatic cell updates)
-- Data visualisation with popular libraries
-- Markdown and LaTeX support
-- Layout components (columns, tabs, accordions)
-- Forms and user input handling
-- Dynamic content generation
-
-Run this notebook with: marimo edit rhiza.py
-Or in the rhiza project: make marimo
-"""
-
-# /// script
-# requires-python = ">=3.11"
-# dependencies = [
-#     "marimo==0.18.4",
-#     "numpy>=1.24.0",
-#     "plotly>=5.18.0",
-#     "pandas>=2.0.0",
-# ]
-# ///
-
-import marimo
-
-__generated_with = "0.18.4"
-app = marimo.App(width="medium")
-
-with app.setup:
-    import marimo as mo
-    import numpy as np
-    import pandas as pd
-    import plotly.graph_objects as go
-
-
-@app.cell
-def cell_02():
-    """Render the showcase introduction Markdown content."""
-    mo.md(
-        r"""
-        # 🎨 Marimo Showcase
-
-        Welcome to the **Marimo Showcase Notebook**! This interactive notebook demonstrates
-        the most powerful and useful features of [Marimo](https://marimo.io/).
-
-        **Marimo** is a reactive Python notebook that combines the best of Jupyter notebooks
-        with the power of reactive programming. Every cell automatically updates when its
-        dependencies change, creating a seamless interactive experience.
-
-        ## Why Marimo?
-
-        - ✨ **Reactive by default** - No manual cell re-runs
-        - 🎯 **Pure Python** - Notebooks are `.py` files
-        - 🔄 **Reproducible** - Consistent execution order
-        - 🎨 **Rich UI elements** - Beautiful interactive components
-        - 📦 **Version control friendly** - Easy to diff and merge
-        """
-    )
-
-
-@app.cell
-def cell_03():
-    """Render a horizontal rule to separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_04():
-    """Introduce the Interactive UI Elements section."""
-    mo.md(
-        r"""
-        ## 🎚️ Interactive UI Elements
-
-        Marimo provides rich UI components that automatically trigger reactive updates.
-        """
-    )
-
-
-@app.cell
-def cell_05():
-    """Create and display a numeric slider UI component."""
-    # Slider for numeric input
-    slider = mo.ui.slider(start=0, stop=100, value=50, label="Adjust the value:", show_value=True)
-    slider
-    return (slider,)
-
-
-@app.cell
-def cell_06(slider):
-    """Display the current slider value reactively."""
-    mo.md(
-        f"""
-        The slider value is: **{slider.value}**
-
-        This text updates automatically when you move the slider! ✨
-        """
-    )
-
-
-@app.cell
-def cell_07():
-    """Create and display a dropdown for language selection."""
-    # Dropdown for selection
-    dropdown = mo.ui.dropdown(
-        options=["Python", "JavaScript", "Rust", "Go", "TypeScript"],
-        value="Python",
-        label="Choose your favorite language:",
-    )
-    dropdown
-    return (dropdown,)
-
-
-@app.cell
-def cell_08(dropdown):
-    """Display the currently selected language from the dropdown."""
-    mo.md(
-        f"""
-        You selected: **{dropdown.value}** 🎉
-
-        Great choice! {dropdown.value} is an excellent programming language.
-        """
-    )
-
-
-@app.cell
-def cell_09():
-    """Create and display a text input field for the user's name."""
-    # Text input
-    text_input = mo.ui.text(value="Marimo", label="Enter your name:", placeholder="Type something...")
-    text_input
-    return (text_input,)
-
-
-@app.cell
-def cell_10(text_input):
-    """Display a personalized greeting using the current text input value."""
-    mo.md(f"""Hello, **{text_input.value}**! 👋""")
-
-
-@app.cell
-def cell_11():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_12():
-    """Introduce the Data Visualisation section."""
-    mo.md(
-        r"""
-        ## 📊 Data Visualisation
-
-        Marimo works seamlessly with popular visualisation libraries like Plotly,
-        Altair, and Matplotlib. Let's create interactive plots!
-        """
-    )
-
-
-@app.cell
-def cell_14():
-    """Create sliders for wave frequency and amplitude controls for the plot."""
-    # Interactive controls for the plot
-    frequency_slider = mo.ui.slider(start=1, stop=10, value=2, label="Wave frequency:", show_value=True)
-
-    amplitude_slider = mo.ui.slider(start=1, stop=5, value=1, label="Wave amplitude:", show_value=True)
-
-    mo.vstack([frequency_slider, amplitude_slider])
-    return amplitude_slider, frequency_slider
-
-
-@app.cell
-def cell_15(amplitude_slider, frequency_slider):
-    """Build a reactive Plotly sine wave based on the slider values."""
-    # Generate reactive plot based on slider values
-    x = np.linspace(0, 4 * np.pi, 1000)
-    y = amplitude_slider.value * np.sin(frequency_slider.value * x)
-
-    fig = go.Figure()
-    fig.add_trace(go.Scatter(x=x, y=y, mode="lines", line={"color": "#2FA4A9", "width": 2}, name="Sine Wave"))
-
-    fig.update_layout(
-        title=f"Sine Wave: y = {amplitude_slider.value} × sin({frequency_slider.value}x)",
-        xaxis_title="x",
-        yaxis_title="y",
-        template="plotly_white",
-        height=400,
-        showlegend=False,
-    )
-
-    fig.update_xaxes(showgrid=True, gridwidth=1, gridcolor="rgba(128,128,128,0.2)")
-    fig.update_yaxes(showgrid=True, gridwidth=1, gridcolor="rgba(128,128,128,0.2)")
-
-    mo.vstack(
-        [
-            mo.md(
-                f"""
-            ### Interactive Sine Wave
-
-            Adjust the sliders above to change the wave properties!
-
-            Current parameters:
-            - Frequency: {frequency_slider.value}
-            - Amplitude: {amplitude_slider.value}
-            """
-            ),
-            mo.ui.plotly(fig),
-        ]
-    )
-    return fig, x, y
-
-
-@app.cell
-def cell_16():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_17():
-    """Introduce the DataFrames section."""
-    mo.md(
-        r"""
-        ## 📋 Working with DataFrames
-
-        Marimo provides excellent support for working with Pandas DataFrames.
-        """
-    )
-
-
-@app.cell
-def cell_18():
-    """Create a sample Pandas DataFrame for use in subsequent cells."""
-    # Create sample data
-    data = pd.DataFrame(
-        {
-            "Product": ["Widget A", "Widget B", "Widget C", "Widget D", "Widget E"],
-            "Sales": [250, 180, 420, 350, 290],
-            "Revenue": [5000, 3600, 8400, 7000, 5800],
-            "Rating": [4.5, 4.2, 4.8, 4.6, 4.3],
-        }
-    )
-    return data
-
-
-@app.cell
-def cell_19():
-    """Render introductory text for the sample sales dataset."""
-    mo.md(
-        r"""
-        ### Sample Sales Data
-
-        Here's our dataset displayed as an interactive table:
-        """
-    )
-
-
-@app.cell
-def cell_20(data):
-    """Display the sample dataset as an interactive table."""
-    # Display as interactive table
-    mo.ui.table(data)
-
-
-@app.cell
-def cell_21(data):
-    """Render a Plotly bar chart showing sales by product."""
-    # Create a bar chart with Plotly
-    colours = ["#2FA4A9", "#3FB5BA", "#4FC6CB", "#5FD7DC", "#6FE8ED"]
-
-    fig_bar = go.Figure()
-    fig_bar.add_trace(
-        go.Bar(
-            x=data["Product"],
-            y=data["Sales"],
-            marker_color=colours,
-            text=data["Sales"],
-            textposition="auto",
-        )
-    )
-
-    fig_bar.update_layout(
-        title="Sales by Product",
-        xaxis_title="Product",
-        yaxis_title="Sales",
-        template="plotly_white",
-        height=500,
-        showlegend=False,
-    )
-
-    mo.ui.plotly(fig_bar)
-    return colours, fig_bar
-
-
-@app.cell
-def cell_22():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_23():
-    """Introduce the layout components section."""
-    mo.md(
-        r"""
-        ## 🎯 Layout Components
-
-        Marimo provides powerful layout primitives to organise your content.
-        """
-    )
-
-
-@app.cell
-def cell_24():
-    """Demonstrate a two-column layout with left and right content."""
-    # Using columns for side-by-side layout
-    left_content = mo.md(
-        r"""
-        ### Left Column
-
-        This is the left side of a two-column layout.
-
-        - Feature 1
-        - Feature 2
-        - Feature 3
-        """
-    )
-
-    right_content = mo.md(
-        r"""
-        ### Right Column
-
-        This is the right side of a two-column layout.
-
-        - Benefit A
-        - Benefit B
-        - Benefit C
-        """
-    )
-
-    mo.hstack([left_content, right_content], justify="space-between")
-    return left_content, right_content
-
-
-@app.cell
-def cell_25():
-    """Demonstrate tabs with Introduction, Details, and Summary content."""
-    # Using tabs for organised content
-    tab1 = mo.md(
-        r"""
-        ## Tab 1: Introduction
-
-        This is the content of the first tab. Tabs are great for organising
-        related content without cluttering the interface.
-
-        **Key points:**
-        - Clean organisation
-        - Reduced clutter
-        - Easy navigation
-        """
-    )
-
-    tab2 = mo.md(
-        r"""
-        ## Tab 2: Details
-
-        Here's more detailed information in the second tab.
-
-        You can include any content here:
-        - Code examples
-        - Visualisations
-        - Interactive elements
-        """
-    )
-
-    tab3 = mo.md(
-        r"""
-        ## Tab 3: Summary
-
-        The final tab with summary information.
-
-        Tabs are perfect for:
-        1. Step-by-step guides
-        2. Different views of data
-        3. Organising complex notebooks
-        """
-    )
-
-    mo.ui.tabs({"Introduction": tab1, "Details": tab2, "Summary": tab3})
-    return tab1, tab2, tab3
-
-
-@app.cell
-def cell_26():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_27():
-    """Introduce the forms and user input section."""
-    mo.md(
-        r"""
-        ## 📝 Forms and User Input
-
-        Marimo forms allow you to batch multiple inputs and submit them together.
-        """
-    )
-
-
-@app.cell
-def cell_28():
-    """Build and display a multi-input form for collecting user information."""
-    # Create a form with multiple inputs
-    form = mo.ui.dictionary(
-        {
-            "name": mo.ui.text(label="Your name:", placeholder="Enter name"),
-            "age": mo.ui.slider(start=18, stop=100, value=25, label="Your age:"),
-            "email": mo.ui.text(label="Email:", placeholder="email@example.com"),
-            "subscribe": mo.ui.checkbox(label="Subscribe to newsletter"),
-            "interests": mo.ui.multiselect(
-                options=["Data Science", "Machine Learning", "Web Development", "DevOps"], label="Your interests:"
-            ),
-        }
-    )
-    mo.vstack([mo.md("### User Information Form"), form])
-    return (form,)
-
-
-@app.cell
-def cell_29(form):
-    """Display current form values reactively as the user edits the form."""
-    # Display form values - updates reactively as you type/change values
-    if form.value and any(form.value.values()):
-        interests_text = ", ".join(form.value["interests"]) if form.value["interests"] else "None selected"
-
-        mo.md(
-            f"""
-            ### Current Form Values ✅
-
-            The values update automatically as you interact with the form!
-
-            - **Name:** {form.value["name"] or "(not entered)"}
-            - **Age:** {form.value["age"]}
-            - **Email:** {form.value["email"] or "(not entered)"}
-            - **Newsletter:** {"Subscribed ✅" if form.value["subscribe"] else "Not subscribed"}
-            - **Interests:** {interests_text}
-
-            Notice how the values update reactively as you change them!
-            """
-        )
-    else:
-        mo.md("*The form values will appear here as you interact with them.*")
-
-
-@app.cell
-def cell_30():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_31():
-    """Introduce the Markdown and LaTeX support section."""
-    mo.md(
-        r"""
-        ## 🎓 Markdown & LaTeX Support
-
-        Marimo has excellent support for rich text formatting using Markdown and LaTeX.
-        """
-    )
-
-
-@app.cell
-def cell_32():
-    """Render rich Markdown with LaTeX equations, code blocks, and formatting examples."""
-    mo.md(
-        r"""
-        ### Mathematical Equations
-
-        You can write beautiful equations using LaTeX:
-
-        **Pythagorean theorem:**
-
-        $$a^2 + b^2 = c^2$$
-
-        **Euler's identity:**
-
-        $$e^{i\pi} + 1 = 0$$
-
-        **Quadratic formula:**
-
-        $$x = \frac{-b \pm \sqrt{b^2 - 4ac}}{2a}$$
-
-        **Inline math:** The famous $E = mc^2$ equation by Einstein.
-
-        ### Code Blocks
-
-        You can also include syntax-highlighted code:
-
-        ```python
-        def fibonacci(n):
-            if n <= 1:
-                return n
-            return fibonacci(n-1) + fibonacci(n-2)
-        ```
-
-        ### Rich Formatting
-
-        - **Bold text**
-        - *Italic text*
-        - ~~Strikethrough text~~
-        - `Inline code`
-        - [Links](https://marimo.io/)
-
-        > This is a blockquote with important information!
-        """
-    )
-
-
-@app.cell
-def cell_33():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_34():
-    """Introduce the Advanced Features section."""
-    mo.md(
-        r"""
-        ## 🎪 Advanced Features
-
-        Here are some more advanced Marimo features worth exploring.
-        """
-    )
-
-
-@app.cell
-def cell_35():
-    """Render an informational callout about Marimo notebooks being plain Python files."""
-    # Callout boxes for important information
-    mo.callout(
-        mo.md(
-            r"""
-            ### 💡 Pro Tip
-
-            Marimo notebooks are **just Python files**! This means:
-            - Easy version control with Git
-            - Standard code review workflows
-            - No hidden JSON metadata
-            - Compatible with all Python tools
-            """
-        ),
-        kind="info",
-    )
-
-
-@app.cell
-def cell_36():
-    """Display an accordion with notes on reactivity, performance, and dependencies."""
-    # Accordion for collapsible content
-    mo.accordion(
-        {
-            "🔍 Click to learn about Reactive Programming": mo.md(
-                r"""
-            Marimo uses **reactive programming** to automatically track dependencies
-            between cells. When you change a value in one cell, all dependent cells
-            automatically update!
-
-            This eliminates the common notebook problem of running cells out of order.
-            """
-            ),
-            "🚀 Click to learn about Performance": mo.md(
-                r"""
-            Marimo only re-runs cells that are affected by changes, making it
-            efficient even for large notebooks. This intelligent execution means
-            you get fast feedback without wasting computation.
-            """
-            ),
-            "📦 Click to learn about Dependencies": mo.md(
-                r"""
-            You can specify dependencies right in the notebook using inline metadata.
-            This makes notebooks self-contained and reproducible, as seen in the
-            header of this notebook!
-            """
-            ),
-        }
-    )
-
-
-@app.cell
-def cell_37():
-    """Render a horizontal rule to visually separate sections."""
-    mo.md(r"""---""")
-
-
-@app.cell
-def cell_38():
-    """Render the conclusion section of the Marimo showcase notebook."""
-    mo.md(
-        r"""
-        ## 🎉 Conclusion
-
-        This notebook has demonstrated many of Marimo's most useful features:
-
-        ✅ **Interactive UI elements** - Sliders, dropdowns, text inputs, and more
-        ✅ **Reactive programming** - Automatic cell updates when dependencies change
-        ✅ **Data visualisation** - Seamless integration with Plotly, Matplotlib, etc.
-        ✅ **Layout components** - Columns, tabs, accordions for organising content
-        ✅ **Forms** - Batched input collection with submission
-        ✅ **Rich formatting** - Markdown and LaTeX support
-        ✅ **Pure Python** - Notebooks are version-control friendly `.py` files
-
-        ### Next Steps
-
-        To learn more about Marimo:
-        - Visit the [official documentation](https://docs.marimo.io/)
-        - Explore the [example gallery](https://marimo.io/examples)
-        - Join the [community Discord](https://discord.gg/JE7nhX6mD8)
-
-        **Happy exploring! 🚀**
-        """
-    )
-
-
-if __name__ == "__main__":
-    app.run()
diff --git a/book/minibook-templates/custom.html.jinja2 b/book/minibook-templates/custom.html.jinja2
deleted file mode 100644
index eda66e9b..00000000
--- a/book/minibook-templates/custom.html.jinja2
+++ /dev/null
@@ -1,210 +0,0 @@
-<! DOCTYPE html>
-<html lang="en" class="dark">
-<head>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>{{ title }}</title>
-    <script src="https://cdn.tailwindcss.com"></script>
-    <script>
-        tailwind.config = {
-            darkMode: 'class',
-            theme: {
-                extend:  {
-                    animation: {
-                        'gradient': 'gradient 15s ease infinite',
-                    },
-                    keyframes:  {
-                        gradient: {
-                            '0%, 100%': { backgroundPosition: '0% 50%' },
-                            '50%': { backgroundPosition:  '100% 50%' },
-                        }
-                    }
-                }
-            }
-        }
-    </script>
-    <style>
-        @import url('https://fonts.googleapis.com/css2?family=Inter: wght@300;400;500;600;700&display=swap');
-
-        body {
-            font-family: 'Inter', sans-serif;
-        }
-
-        .link-card {
-            /* Animation removed as requested */
-        }
-
-        .gradient-text {
-            background-clip: text;
-            -webkit-background-clip:  text;
-            color: transparent;
-            background-image: linear-gradient(to right, #6366f1, #8b5cf6, #d946ef);
-        }
-
-        /* Logo styling */
-        .logo-img {
-            max-height: 60px;
-            width: auto;
-        }
-
-        /* Light mode styles */
-        html:not(.dark) body {
-            background-color: #f9fafb;
-            color:  #1f2937;
-        }
-
-        html:not(.dark) .theme-container {
-            background: linear-gradient(to bottom right, #f3f4f6, #e5e7eb, #f3f4f6);
-        }
-
-        html: not(.dark) .content-container {
-            background-color: rgba(255, 255, 255, 0.8);
-            border-color: #e5e7eb;
-        }
-
-        html:not(.dark) .link-card a {
-            background-color: rgba(243, 244, 246, 0.5);
-            border-color: #e5e7eb;
-        }
-
-        html:not(.dark) .link-card a:hover {
-            background-color: rgba(249, 250, 251, 0.5);
-            border-color: #6366f1;
-        }
-
-        html:not(.dark) .card-title {
-            color: #1f2937;
-        }
-
-        html:not(.dark) .card-url {
-            color:  #6b7280;
-        }
-
-        html:not(.dark) .footer-border {
-            border-color: #e5e7eb;
-        }
-
-        html:not(.dark) .footer-text {
-            color: #6b7280;
-        }
-    </style>
-    <script>
-        // Check for saved theme preference or use default (dark)
-        document.addEventListener('DOMContentLoaded', () => {
-            const theme = localStorage.getItem('theme') || 'dark';
-            document.documentElement. className = theme;
-
-            // Update toggle button appearance
-            updateToggleButton();
-        });
-
-        // Toggle between dark and light themes
-        function toggleTheme() {
-            const html = document.documentElement;
-            const newTheme = html.classList.contains('dark') ? '' : 'dark';
-
-            html.className = newTheme;
-            localStorage.setItem('theme', newTheme);
-
-            // Update toggle button appearance
-            updateToggleButton();
-        }
-
-        // Update toggle button icon based on current theme
-        function updateToggleButton() {
-            const isDark = document.documentElement.classList. contains('dark');
-            const sunIcon = document.getElementById('sun-icon');
-            const moonIcon = document.getElementById('moon-icon');
-
-            if (isDark) {
-                sunIcon.classList.remove('hidden');
-                moonIcon. classList.add('hidden');
-            } else {
-                sunIcon. classList.add('hidden');
-                moonIcon.classList.remove('hidden');
-            }
-        }
-    </script>
-</head>
-<body class="dark:bg-black dark:text-gray-200 text-gray-800 font-sans leading-normal tracking-normal min-h-screen">
-    <div class="theme-container dark:bg-gradient-to-br dark:from-gray-900 dark:via-gray-800 dark:to-gray-900 min-h-screen py-12 px-4 sm: px-6 dark:animate-gradient dark:bg-[length: 200%_200%]">
-        <div class="content-container container max-w-4xl mx-auto backdrop-blur-sm dark:bg-black/30 rounded-xl shadow-2xl p-8 border dark:border-gray-800">
-            
-            <!-- LOGO SECTION - ADD THIS -->
-            <div class="flex justify-center mb-6">
-                <img src="https://raw.githubusercontent.com/Jebel-Quant/rhiza/main/assets/rhiza-logo.svg" alt="Logo" class="logo-img">
-            </div>
-            <!-- END LOGO SECTION -->
-
-            <div class="flex items-center justify-between mb-8">
-                <div>
-                    <h1 class="text-4xl font-bold mb-2 gradient-text">{{ title }}</h1>
-                    {% if description %}
-                    <div class="dark:text-gray-400 text-gray-600 italic">{{ description }}</div>
-                    {% endif %}
-                </div>
-                <div class="flex items-center space-x-4">
-                    <button onclick="toggleTheme()" class="flex items-center px-3 py-2 rounded-lg dark: bg-gray-800 bg-gray-200 border dark:border-gray-700 border-gray-300 hover:border-indigo-500 transition-colors duration-200">
-                        <!-- Sun icon for dark mode (shows when in dark mode) -->
-                        <svg id="sun-icon" xmlns="http://www.w3.org/2000/svg" class="h-5 w-5 mr-2 text-yellow-400" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 3v1m0 16v1m9-9h-1M4 12H3m15.364 6.364l-.707-.707M6.343 6.343l-.707-.707m12.728 0l-.707.707M6.343 17.657l-.707.707M16 12a4 4 0 11-8 0 4 4 0 018 0z" />
-                        </svg>
-                        <!-- Moon icon for light mode (shows when in light mode) -->
-                        <svg id="moon-icon" xmlns="http://www.w3.org/2000/svg" class="h-5 w-5 mr-2 text-indigo-600 hidden" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M20.354 15.354A9 9 0 018.646 3.646 9.003 9.003 0 0012 21a9.003 9.003 0 008.354-5.646z" />
-                        </svg>
-                        <span class="dark:text-white text-gray-800 text-sm font-medium">Toggle Theme</span>
-                    </button>
-                    <a href="{{ repository_url }}" target="_blank" class="flex items-center px-3 py-2 rounded-lg dark:bg-gray-800 bg-gray-200 border dark:border-gray-700 border-gray-300 hover:border-indigo-500 transition-colors duration-200">
-                        <svg xmlns="http://www.w3.org/2000/svg" class="h-5 w-5 mr-2 dark:text-indigo-400 text-indigo-600" fill="currentColor" viewBox="0 0 24 24">
-                            <path d="M12 0c-6.626 0-12 5.373-12 12 0 5.302 3.438 9.8 8.207 11.387.599.111.793-.261.793-.577v-2.234c-3.338.726-4.033-1.416-4.033-1.416-.546-1.387-1.333-1.756-1.333-1.756-1.089-.745.083-.729.083-.729 1.205.084 1.839 1.237 1.839 1.237 1.07 1.834 2.807 1.304 3.492.997.107-.775.418-1.305.762-1.604-2.665-.305-5.467-1.334-5.467-5.931 0-1.311.469-2.381 1.236-3.221-.124-.303-.535-1.524.117-3.176 0 0 1.008-.322 3.301 1.23.957-.266 1.983-.399 3.003-.404 1.02.005 2.047.138 3.006.404 2.291-1.552 3.297-1.23 3.297-1.23.653 1.653.242 2.874.118 3.176.77.84 1.235 1.911 1.235 3.221 0 4.609-2.807 5.624-5.479 5.921.43.372.823 1.102.823 2.222v3.293c0 .319.192.694.801.576 4.765-1.589 8.199-6.086 8.199-11.386 0-6.627-5.373-12-12-12z"/>
-                        </svg>
-                        <span class="dark:text-white text-gray-800 text-sm font-medium">Home Repo</span>
-                    </a>
-                </div>
-            </div>
-
-            <div class="grid grid-cols-1 md: grid-cols-2 gap-4 mb-8">
-                {% for name, url in links %}
-                <div class="link-card group">
-                    <a href="{{ url }}" target="_blank" class="block p-4 rounded-lg dark:bg-gray-800/50 bg-gray-100/80 border dark:border-gray-700 border-gray-300 dark:hover:border-indigo-500 hover: border-indigo-600 transition-all duration-200">
-                        <div class="flex items-center">
-                            <div class="flex-shrink-0 w-10 h-10 rounded-full bg-gradient-to-r from-indigo-500 to-purple-600 flex items-center justify-center mr-4 group-hover:from-purple-600 group-hover:to-pink-600 transition-all duration-200">
-                                <span class="text-white font-bold">{{ name[0] | upper }}</span>
-                            </div>
-                            <div>
-                                <h3 class="card-title text-lg font-medium dark:text-white text-gray-800 dark:group-hover:text-indigo-300 group-hover:text-indigo-600 transition-colors duration-200">{{ name }}</h3>
-                                <p class="card-url text-xs dark:text-gray-400 text-gray-500 truncate">{{ url }}</p>
-                            </div>
-                        </div>
-                    </a>
-                </div>
-                {% endfor %}
-            </div>
-
-            <div class="mt-12 pt-6 border-t footer-border dark:border-gray-800 border-gray-300 text-center">
-                <div class="footer-text dark:text-gray-500 text-gray-600 text-sm mb-2">
-                    Generated by <a href="https://pypi.org/project/minibook/" class="dark:text-indigo-400 text-indigo-600 dark:hover:text-indigo-300 hover: text-indigo-500 transition-colors duration-200 font-medium">MiniBook</a> on {{ timestamp }}
-                </div>
-                <div class="flex items-center justify-center space-x-2 mb-2">
-                    <span class="footer-text dark:text-gray-500 text-gray-600">A product by</span>
-                    <a href="https://jqr.ae" class="dark:text-indigo-400 text-indigo-600 dark:hover:text-indigo-300 hover: text-indigo-500 transition-colors duration-200 font-medium flex items-center">
-                        jqr
-                        <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 ml-1" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14" />
-                        </svg>
-                    </a>
-                </div>
-                <div class="flex items-center justify-center">
-                    <a href="https://pypi.org/project/minibook/" class="dark:text-indigo-400 text-indigo-600 dark:hover:text-indigo-300 hover:text-indigo-500 transition-colors duration-200 font-medium flex items-center">
-                        PyPI Package
-                        <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 ml-1" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M10 6H6a2 2 0 00-2 2v10a2 2 0 002 2h10a2 2 0 002-2v-4M14 4h6m0 0v6m0-6L10 14" />
-                        </svg>
-                    </a>
-                </div>
-            </div>
-        </div>
-    </div>
-</body>
-</html>
\ No newline at end of file
diff --git a/docs/assets/rhiza-logo.svg b/docs/assets/rhiza-logo.svg
new file mode 100644
index 00000000..ff1c9f57
--- /dev/null
+++ b/docs/assets/rhiza-logo.svg
@@ -0,0 +1,81 @@
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+<path d="" fill="#008080" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#008080" transform="translate(0,0)"/>
+<path d="" fill="#008080" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#0080FF" transform="translate(0,0)"/>
+<path d="" fill="#008080" transform="translate(0,0)"/>
+<path d="" fill="#00BFBF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#0080FF" transform="translate(0,0)"/>
+<path d="" fill="#0080FF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#008080" transform="translate(0,0)"/>
+<path d="" fill="#00AAAA" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#0080FF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#00BFBF" transform="translate(0,0)"/>
+<path d="" fill="#00FFFF" transform="translate(0,0)"/>
+<path d="" fill="#008080" transform="translate(0,0)"/>
+</svg>
diff --git a/book/marimo/README.md b/docs/development/MARIMO.md
similarity index 95%
rename from book/marimo/README.md
rename to docs/development/MARIMO.md
index d9eb024c..df69cce7 100644
--- a/book/marimo/README.md
+++ b/docs/development/MARIMO.md
@@ -33,14 +33,14 @@ From the repository root:
 make marimo
 ```
 
-This will start the Marimo server and open all notebooks in the `book/marimo` directory.
+This will start the Marimo server and open all notebooks in the `docs/notebooks` directory.
 
 ### Running a Specific Notebook
 
 To run a single notebook:
 
 ```bash
-marimo edit book/marimo/rhiza.py
+marimo edit docs/notebooks/rhiza.py
 ```
 
 ### Using uv (Recommended)
@@ -48,7 +48,7 @@ marimo edit book/marimo/rhiza.py
 The notebooks include inline dependency metadata, making them self-contained:
 
 ```bash
-uv run book/marimo/rhiza.py
+uv run docs/notebooks/rhiza.py
 ```
 
 This will automatically install the required dependencies and run the notebook.
@@ -100,7 +100,7 @@ To create a new Marimo notebook:
 
 1. Create a new `.py` file in this directory:
    ```bash
-   marimo edit book/marimo/my_notebook.py
+   marimo edit docs/notebooks/my_notebook.py
    ```
 
 2. Add inline metadata at the top:
@@ -118,7 +118,7 @@ To create a new Marimo notebook:
 
 4. Test it runs in a clean environment:
    ```bash
-   uv run book/marimo/my_notebook.py
+   uv run docs/notebooks/my_notebook.py
    ```
 
 5. Commit and push - the CI will validate it automatically
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..0e0b6b49
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,2 @@
+--8<-- "README.md"
+
diff --git a/docs/mkdocs-base.yml b/docs/mkdocs-base.yml
new file mode 100644
index 00000000..6d7143d9
--- /dev/null
+++ b/docs/mkdocs-base.yml
@@ -0,0 +1,71 @@
+# docs/mkdocs-base.yml — Base MkDocs configuration for rhiza-based projects.
+#
+# USAGE (standalone)
+#   Build or serve this file directly if you have no root-level mkdocs.yml:
+#     uvx --with mkdocs-material mkdocs serve -f docs/mkdocs-base.yml
+#   The rhiza build system (make book) will pick this file up automatically
+#   as a fallback when no root-level mkdocs.yml is found.
+#
+# USAGE (with INHERIT)
+#   To extend this config from a root-level mkdocs.yml, add the following
+#   at the top of your mkdocs.yml and override only what you need:
+#
+#     INHERIT: docs/mkdocs-base.yml
+#
+#     site_name: My Project
+#     site_url: https://example.github.io/my-project/
+#     repo_url: https://github.com/example/my-project
+#     repo_name: example/my-project
+#
+#     docs_dir: docs   # always set this explicitly — base uses docs_dir: . which
+#                      # resolves relative to docs/mkdocs-base.yml, not mkdocs.yml
+#
+#     nav:             # nav is fully replaced — not merged — by the child config
+#       - Home: index.md
+#       - Guide: guide.md
+#
+#   Any key you omit in mkdocs.yml is inherited from this file.
+#   The 'nav' key is always fully replaced when defined in the child.
+
+site_name: Rhiza
+docs_dir: .
+site_dir: _mkdocs
+
+theme:
+  name: material
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - navigation.top
+    - search.suggest
+    - search.highlight
+  logo: assets/rhiza-logo.svg
+  favicon: assets/rhiza-logo.svg
+
+plugins:
+  - search
+
+markdown_extensions:
+  - md_in_html
+  - pymdownx.highlight
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.snippets:
+      base_path: ["."]
+  - admonition
+  - toc:
+      permalink: true
+      toc_depth: 3
+
+extra_javascript:
+  - https://unpkg.com/mermaid@11.4.0/dist/mermaid.esm.min.mjs
+
+# nav is overwritten completely in mkdocs.yml
+nav:
+  - Home: index.md
+  - Notebooks: notebooks.md
+  - Reports: reports.md
+  - Paper: paper/rhiza.pdf
diff --git a/renovate.json b/renovate.json
deleted file mode 100644
index 2d59f362..00000000
--- a/renovate.json
+++ /dev/null
@@ -1,29 +0,0 @@
-{
-    "extends": [
-        "config:recommended",
-        ":enablePreCommit",
-        ":automergeMinor",
-        ":dependencyDashboard",
-        ":maintainLockFilesWeekly",
-        ":semanticCommits",
-        ":pinDevDependencies"
-    ],
-    "enabledManagers": [
-        "pep621",
-        "pre-commit",
-        "github-actions",
-        "devcontainer",
-        "dockerfile"
-    ],
-    "timezone": "Asia/Dubai",
-    "schedule": [
-        "before 10am on tuesday"
-    ],
-    "packageRules": [
-      {
-        "matchManagers": ["pep621"],
-        "matchPackageNames": ["python"],
-        "enabled": false
-      }
-    ]
-}
diff --git a/ruff.toml b/ruff.toml
index f99a9933..4563178d 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -69,10 +69,10 @@ extend-select = [
     "D107",  # pydocstyle - Require docstrings for __init__
     "B",     # flake8-bugbear - Find likely bugs and design problems
     "C4",    # flake8-comprehensions - Better list/set/dict comprehensions
-    #"SIM",   # flake8-simplify - Simplify code
+    "SIM",   # flake8-simplify - Simplify code
     "PT",    # flake8-pytest-style - Check pytest best practices
     "RUF",   # Ruff-specific rules
-    #"S",     # flake8-bandit - Find security issues
+    "S",     # flake8-bandit - Find security issues
     #"ERA",   # eradicate - Find commented out code
     #"T10",   # flake8-debugger - Check for debugger imports and calls
     "TRY",   # flake8-try-except-raise - Try/except/raise checks
@@ -101,25 +101,31 @@ line-ending = "auto"
 
 # File-specific rule exceptions
 [lint.per-file-ignores]
-"tests/**/*.py" = [
+# Test files - allow assert statements and subprocess calls for testing
+"**/tests/**/*.py" = [
     "S101",     # Allow assert statements in tests
     "S603",     # Allow subprocess calls without shell=False check
+    "S607",     # Allow starting processes with partial paths in tests
     "PLW1510",  # Allow subprocess without explicit check parameter
-    "ERA001",   # Allow commented out code
-    "PLR2004",  # Allow magic values
-    "RUF002",   # Allow ambiguous unicode
-    "RUF012",   # Allow mutable class attributes
 ]
-# this will also work book/marimo or test/resources/marimo ...
-"**/marimo/**/*.py" = [
-    "N803",    # Allow non-lowercase variable names
-    "S101",    # Allow assert statements
-    "PLC0415", # Allow imports not at top-level
-    "B018",    # Allow useless expressions
-    "RUF001",  # Allow ambiguous unicode
-    "RUF002",  # Allow ambiguous unicode
+"tests/**/*.py" = [
+    "ERA001",   # Allow commented out code in project tests
+    "PLR2004",  # Allow magic values in project tests
+    "RUF002",   # Allow ambiguous unicode in project tests
+    "RUF012",   # Allow mutable class attributes in project tests
+]
+# Marimo notebooks - allow flexible coding patterns for interactive exploration
+"**/notebooks/*.py" = [
+    "D100",    # No module docstring - marimo requires `import marimo` as the first statement
+    "N803",    # Allow non-lowercase variable names in notebooks
+    "S101",    # Allow assert statements in notebooks
+    "PLC0415", # Allow imports not at top-level in notebooks
+    "B018",    # Allow useless expressions in notebooks
+    "RUF001",  # Allow ambiguous unicode in notebooks
+    "RUF002",  # Allow ambiguous unicode in notebooks
 ]
+# Internal utility scripts - specific exceptions for internal tooling
 ".rhiza/utils/*.py" = [
-    "PLW2901",  # Allow loop variable overwriting
-    "TRY003",   # Allow long exception messages
+    "PLW2901",  # Allow loop variable overwriting in utility scripts
+    "TRY003",   # Allow long exception messages in utility scripts
 ]

From 05f0476cf635350a724f684a5306c827509ddad1 Mon Sep 17 00:00:00 2001
From: Thomas Schmelzer <thomas.schmelzer@gmail.com>
Date: Thu, 16 Apr 2026 06:54:15 +0400
Subject: [PATCH 3/5] Remove the README from make.d

---
 .rhiza/make.d/README.md | 82 -----------------------------------------
 1 file changed, 82 deletions(-)
 delete mode 100644 .rhiza/make.d/README.md

diff --git a/.rhiza/make.d/README.md b/.rhiza/make.d/README.md
deleted file mode 100644
index 6f80875a..00000000
--- a/.rhiza/make.d/README.md
+++ /dev/null
@@ -1,82 +0,0 @@
-# Makefile Cookbook
-
-This directory (`.rhiza/make.d/`) is the designated place for **repository-specific build logic**. Any `.mk` file added here is automatically absorbed by the main Makefile.
-
-Use this cookbook to find copy-paste patterns for common development needs.
-
-## 🥘 Recipes
-
-### 1. Add a Simple Task
-**Goal**: Run a script with `make train-model`.
-
-Create `.rhiza/make.d/50-model.mk`:
-```makefile
-##@ Machine Learning
-train: ## Train the model using local data
-	@echo "Training model..."
-	@uv run python scripts/train.py
-```
-
-### 2. Inject Code into Standard Workflows (Hooks)
-**Goal**: Apply task after `make sync`.
-
-Create `.rhiza/make.d/90-hooks.mk`:
-```makefile
-post-sync::
-	@echo "Applying something..."
-```
-*Note: Use double-colons (`::`) for hooks to avoid conflicts.*
-
-### 3. Define Global Variables
-**Goal**: Set a default timeout for all test runs.
-
-Create `.rhiza/make.d/01-config.mk`:
-```makefile
-# Override default timeout (defaults to 60s)
-export TEST_TIMEOUT := 120
-```
-
-### 4. Create a Private Shortcut
-**Goal**: Create a command that only exists on my machine (not committed).
-
-Do not use `.rhiza/make.d/`. Instead, create a `local.mk` in the project root:
-```makefile
-deploy-dev:
-	@./scripts/deploy-to-my-sandbox.sh
-```
-
-### 5. Install System Dependencies
-**Goal**: Ensure `graphviz` is installed for Marimo notebooks using a hook.
-
-Create `.rhiza/make.d/20-dependencies.mk`:
-```makefile
-pre-install::
-	@if ! command -v dot >/dev/null 2>&1; then \
-		echo "Graphviz not found. Installing..."; \
-		if command -v brew >/dev/null 2>&1; then \
-			brew install graphviz; \
-		elif command -v apt-get >/dev/null 2>&1; then \
-			sudo apt-get install -y graphviz; \
-		else \
-			echo "Please install graphviz manually."; \
-			exit 1; \
-		fi \
-	fi
-```
-
----
-
-## ℹ️ Reference
-
-### Execution Order
-Files are loaded alphabetically. We use numeric prefixes to ensure dependencies resolve correctly:
-- `00-19`: Configuration & Variables
-- `20-79`: Custom Tasks & Rules
-- `80-99`: Hooks & Lifecycle logic
-
-### Available Hooks
-- `pre-install` / `post-install`: Runs around `make install`.
-- `pre-sync` / `post-sync`: Runs around repository synchronization.
-- `pre-validate` / `post-validate`: Runs around validation checks.
-- `pre-release` / `post-release`: Runs around release process.
-- `pre-bump` / `post-bump`: Runs around version bumping.

From 3865e437e426c5ff8484cdeb25a40846445737c4 Mon Sep 17 00:00:00 2001
From: Thomas Schmelzer <thomas.schmelzer@gmail.com>
Date: Thu, 16 Apr 2026 06:58:27 +0400
Subject: [PATCH 4/5] moving documents into place

---
 book/docs/index.md                           |   1 -
 {book/docs => docs}/paper/1310.3396.pdf      | Bin
 {book/docs => docs}/paper/SSRN-id2695101.pdf | Bin
 {book/docs => docs}/talk/abstract.txt        |   0
 {book/docs => docs}/talk/bio.txt             |   0
 {book/docs => docs}/talk/title.txt           |   0
 6 files changed, 1 deletion(-)
 delete mode 120000 book/docs/index.md
 rename {book/docs => docs}/paper/1310.3396.pdf (100%)
 rename {book/docs => docs}/paper/SSRN-id2695101.pdf (100%)
 rename {book/docs => docs}/talk/abstract.txt (100%)
 rename {book/docs => docs}/talk/bio.txt (100%)
 rename {book/docs => docs}/talk/title.txt (100%)

diff --git a/book/docs/index.md b/book/docs/index.md
deleted file mode 120000
index fe840054..00000000
--- a/book/docs/index.md
+++ /dev/null
@@ -1 +0,0 @@
-../../README.md
\ No newline at end of file
diff --git a/book/docs/paper/1310.3396.pdf b/docs/paper/1310.3396.pdf
similarity index 100%
rename from book/docs/paper/1310.3396.pdf
rename to docs/paper/1310.3396.pdf
diff --git a/book/docs/paper/SSRN-id2695101.pdf b/docs/paper/SSRN-id2695101.pdf
similarity index 100%
rename from book/docs/paper/SSRN-id2695101.pdf
rename to docs/paper/SSRN-id2695101.pdf
diff --git a/book/docs/talk/abstract.txt b/docs/talk/abstract.txt
similarity index 100%
rename from book/docs/talk/abstract.txt
rename to docs/talk/abstract.txt
diff --git a/book/docs/talk/bio.txt b/docs/talk/bio.txt
similarity index 100%
rename from book/docs/talk/bio.txt
rename to docs/talk/bio.txt
diff --git a/book/docs/talk/title.txt b/docs/talk/title.txt
similarity index 100%
rename from book/docs/talk/title.txt
rename to docs/talk/title.txt

From 0617001b9eecde69a271faf868f824ba4fb87c4a Mon Sep 17 00:00:00 2001
From: Thomas Schmelzer <thomas.schmelzer@gmail.com>
Date: Thu, 16 Apr 2026 06:59:53 +0400
Subject: [PATCH 5/5] reduced Makefile

---
 Makefile | 42 ------------------------------------------
 1 file changed, 42 deletions(-)

diff --git a/Makefile b/Makefile
index 24239e6f..b5fd62f1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,49 +1,7 @@
 ## Makefile (repo-owned)
 # Keep this file small. It can be edited without breaking template sync.
 
-DOCFORMAT=google
-DEFAULT_AI_MODEL=claude-sonnet-4.5
 LOGO_FILE=.rhiza/assets/rhiza-logo.svg
-GH_AW_ENGINE ?= copilot  # Default AI engine for gh-aw workflows (copilot, claude, or codex)
 
 # Always include the Rhiza API (template-managed)
 include .rhiza/rhiza.mk
-
-# Optional: developer-local extensions (not committed)
--include local.mk
-
-# Wire typecheck into make validate
-post-validate::
-	@$(MAKE) typecheck
-
-## Custom targets
-
-.PHONY: adr
-adr: install-gh-aw ## Create a new Architecture Decision Record (ADR) using AI assistance
-	@echo "Creating a new ADR..."
-	@echo "This will trigger the adr-create workflow."
-	@echo ""
-	@read -p "Enter ADR title (e.g., 'Use PostgreSQL for data storage'): " title; \
-	echo ""; \
-	read -p "Enter brief context (optional, press Enter to skip): " context; \
-	echo ""; \
-	if [ -z "$$title" ]; then \
-		echo "Error: Title is required"; \
-		exit 1; \
-	fi; \
-	if [ -z "$$context" ]; then \
-		gh workflow run adr-create.md -f title="$$title"; \
-	else \
-		gh workflow run adr-create.md -f title="$$title" -f context="$$context"; \
-	fi; \
-	echo ""; \
-	echo "✅ ADR creation workflow triggered!"; \
-	echo ""; \
-	echo "The workflow will:"; \
-	echo "  1. Generate the next ADR number"; \
-	echo "  2. Create a comprehensive ADR document"; \
-	echo "  3. Update the ADR index"; \
-	echo "  4. Open a pull request for review"; \
-	echo ""; \
-	echo "Check workflow status: gh run list --workflow=adr-create.md"; \
-	echo "View latest run: gh run view"