move docs around remove irrelevant scripts etc

Author: bwl

AGENTS.md

@@ -8,10 +8,10 @@
 - `forest.db` is a sample database for local smoke tests; feel free to reset it when experimenting.
 
 ## Build, Test, and Development Commands
-- `npm run build` compiles TypeScript to `dist/` with the repo tsconfig.
-- `npm run dev` executes the CLI through `tsx`, ideal for iterating on commands without compiling.
-- `npm run lint` runs `tsc --noEmit` for type safety; treat failures as blockers.
-- `npm start` runs the compiled CLI (`node dist/index.js`); use it when verifying release artifacts.
+- `bun run build` compiles TypeScript to `dist/` with the repo tsconfig.
+- `bun run dev` executes the CLI through `tsx`, ideal for iterating on commands without compiling.
+- `bun run lint` runs `tsc --noEmit` for type safety; treat failures as blockers.
+- `bun run start` runs the compiled CLI (`bun run dist/index.js`); use it when verifying release artifacts.
 
 ## Coding Style & Naming Conventions
 - Follow the existing 2-space indentation, single quotes, and trailing commas where they clarify multi-line structures.
@@ -21,7 +21,7 @@
 ## Testing Guidelines
 - There is no automated test suite yet; for new features, add targeted TypeScript tests alongside the code (e.g., `src/lib/__tests__/graph.spec.ts`) using `tsx` or `ts-node`.
 - Cover edge cases around scoring thresholds, tag extraction, and graph linking; include fixtures under a nearby `fixtures/` folder if needed.
-- Run `npm run dev -- capture --body "example"` against a fresh `forest.db` to perform smoke tests before submitting.
+- Run `bun run dev -- capture --body "example"` against a fresh `forest.db` to perform smoke tests before submitting.
 
 ## Commit & Pull Request Guidelines
 - Write concise, imperative commit subjects (e.g., “Add capture preview summary”), mirroring the existing history.

CLAUDE.md

@@ -86,15 +86,15 @@ cd tldr-agent-spec
 ## Development Commands
 
 ```bash
-npm install          # Install dependencies
-npm run build        # Compile TypeScript to dist/
-npm run lint         # Type-check without emitting files
-npm run dev          # Run from source with ts-node
+bun install          # Install dependencies
+bun run build        # Compile TypeScript to dist/
+bun run lint         # Type-check without emitting files
+bun run dev          # Run from source with ts-node
 
 # Testing the CLI during development
-npm run dev -- capture --stdin < test.txt
-npm run dev -- health
-npm run dev -- stats
+bun run dev -- capture --stdin < test.txt
+bun run dev -- health
+bun run dev -- stats
 
 # Running the API server
 bun run dev:server                    # Start on default port 3000 (dual-stack IPv4/IPv6)

README.md

@@ -5,8 +5,8 @@ A graph-native knowledge base that captures ideas and automatically links them u
 ## Quick Start
 
 ```bash
-npm install
-npm run build
+bun install
+bun run build
 
 # Capture ideas from different sources
 forest capture --stdin < idea.txt
@@ -78,10 +78,16 @@ forest node read abc12345 --raw | glow  # Pipe to markdown viewer
 forest node read abc12345 --json
 ```
 
-**Edit** existing notes:
+**Edit** existing notes with your editor:
 ```bash
-forest node edit abc12345 --title "New title"
-forest node edit abc12345 --stdin < updated.md
+forest node edit abc12345
+forest node edit abc12345 --editor "code --wait"
+```
+
+**Refresh** notes from flags or files:
+```bash
+forest node refresh abc12345 --title "New title"
+forest node refresh abc12345 --stdin < updated.md
 ```
 
 **Synthesize** combines multiple notes into new perspectives:
@@ -397,15 +403,15 @@ TLDR v0.2 provides condensed command metadata optimized for LLM consumption (60%
 
 ```bash
 # Build from source
-npm run build
+bun run build
 
 # Type checking
-npm run lint
+bun run lint
 
 # Run from source
-npm run dev -- capture --stdin
+bun run dev -- capture --stdin
 
-# Start API server (requires Bun)
+# Start API server
 bun run dev:server
 ```
 

bun.lock

@@ -54,8 +54,8 @@ Forest uses a minimal **master + next** branching strategy.
    ```bash
    git checkout next
    # Run tests, verify everything works
-   npm run build
-   npm run lint
+   bun run build
+   bun run lint
    ```
 
 2. **Merge next to master:**
@@ -67,7 +67,7 @@ Forest uses a minimal **master + next** branching strategy.
 3. **Bump version:**
    ```bash
    # Update package.json and src/cli/commands/version.ts
-   npm run build
+   bun run build
    git add package.json src/cli/commands/version.ts
    git commit -m "Bump version to X.Y.Z"
    ```
@@ -127,7 +127,7 @@ git checkout next
 git checkout master
 git merge next
 # Update version files
-npm run build
+bun run build
 git add package.json src/cli/commands/version.ts
 git commit -m "Bump version to 0.3.0"
 git tag -a v0.3.0 -m "Release v0.3.0"

docs/BRANCHING.md

@@ -176,6 +176,7 @@ All commands that accept node refs now support all patterns:
 
 - **`forest node read [ref]`** - Works with `@`, `#tag`, `"title"`, UUID prefix
 - **`forest node edit [ref]`** - Same
+- **`forest node refresh [ref]`** - Same
 - **`forest node delete [ref]`** - Same
 - **`forest node link [ref1] [ref2]`** - Both refs support all patterns
 
@@ -195,7 +196,7 @@ forest node read @<TAB>    # Suggests @, @1, @2, @3, @4, @5
 fpath=(path/to/forest/completions $fpath)
 autoload -Uz compinit && compinit
 
-forest node <TAB>          # Shows: read, edit, delete, link, recent, ...
+forest node <TAB>          # Shows: read, edit, refresh, delete, link, recent, ...
 ```
 
 ## Documentation