v0.22.3 — Manifest-based staleness, path normalization, daemon mode

Overview

Release 0.22.3 replaces the legacy .d dependency-tracking files with a
manifest.json manifest, fixes duplicate file-path entries in the database,
adds daemon mode for background auto-reindexing, and ensures all test fixtures
clean up their index directories after tests.

IMPORTANT: After upgrading, run fw-context index --force on each project
to rebuild the index with the new manifest format and correctly normalized
file paths.

Changes

Features

• manifest.json replaces .d files — a single manifest.json in the index
  directory tracks every translation unit: source hashes, header hashes,
  generated/SDK markers, and staleness checks. This replaces per-TU .d
  files that were scattered across the build tree and often stale.
  The compile_commands.json config hash is now the manifest hash, making
  staleness detection consistent and reliable.
• Daemon mode for background auto-reindex — the MCP server can now run a
  background daemon that watches for file changes and reindexes stale
  translation units automatically. Controlled via the [daemon] config
  section.
• manifest.json verification — fw-context index records a
  manifest_verification status (full / partial / unverified) in the
  build config, giving tooling visibility into index completeness.

Fixes

• Normalize file paths in files table to prevent duplicates — file paths
  are now consistently normalized to project-relative form, preventing the
  same file from appearing under both an absolute and relative path in the
  files table.
• _normalize_file_path resolves project_root before relativizing — fixes
  an edge case where a non-resolved root produced incorrect relative paths.
  Applied consistently across ops, maintenance, and fallback modules.

Refactoring

• dep_files.py removed (151 lines) — replaced by indexer/manifest.py
  (503 lines). The new module uses content hashing over the source file +
  its transitive project headers, with SDK and generated headers excluded
  from staleness checks.
• All 11 builders updated — each builder (arduino, cmake, esp_idf,
  iar, keil, makefile, manual, mbed_os, platformio, zephyr,
  stubs) now generates entries for the manifest during the build step.
• Staleness detection rewritten — shared/stale.py now uses the manifest
  instead of .d files, with trusted-SDK-header and generated-header
  exclusion logic.
• Config hash computation — config_hash.py now derives the hash from the
  manifest (compiler arguments, source file set), excluding source content
  hashes so formatting-only changes don't trigger a full reindex.
• fw-context init --project replaces project-init — the project-init
  command was removed in favor of init --project.
• MCP server maintenance endpoint — /maintenance returns manifest
  verification status and stale file details for health-check tooling.

Maintenance

• Test fixtures clean up index directories — 8 class-scoped fixtures in
  test_system_indexing.py and 4 fixtures/tests in test_index_integrity.py
  now delete their ~/.fw-context/index/<project_id>/ directories after
  tests finish, preventing accumulation of stale multi-GB test indexes.

Documentation

• docs/installation.md — updated for manifest-based workflow
• docs/tools.md — updated tool descriptions to reflect new capabilities

New files

File	Purpose
src/fw_context_mcp/indexer/manifest.py	Manifest generation, loading, staleness checks
tests/test_manifest.py	335-line test suite for manifest operations

Removed files

File	Reason
src/fw_context_mcp/indexer/dep_files.py	Replaced by manifest.py
tests/test_dep_file.py	Replaced by test_manifest.py
src/fw_context_mcp/mcp/shared/context.py	Unused shared context helpers

Changed files

File	Change
src/fw_context_mcp/cli.py	init --project, daemon control
src/fw_context_mcp/indexer/builders/*.py	All 11 builders emit manifest entries
src/fw_context_mcp/indexer/config_hash.py	Manifest-based hash
src/fw_context_mcp/indexer/db.py	Schema for manifest metadata
src/fw_context_mcp/indexer/ops.py	Path normalization, manifest integration
src/fw_context_mcp/indexer/runner.py	Manifest generation pipeline
src/fw_context_mcp/indexer/validator.py	Manifest-aware validation
src/fw_context_mcp/mcp/daemon.py	Background auto-reindex daemon
src/fw_context_mcp/mcp/handlers/maintenance.py	Manifest verification, reindex with normalization
src/fw_context_mcp/mcp/handlers/search.py	Manifest-aware staleness
src/fw_context_mcp/mcp/shared/stale.py	Manifest-based staleness detection
src/fw_context_mcp/utils.py	Shared helpers for path ops
tests/test_incremental_reindex.py	Expanded reindex coverage with manifest
tests/test_index_integrity.py	Manifest verification in integrity tests
tests/test_system_indexing.py	Manifest verification + index cleanup
tests/test_builders/*.py	Updated for manifest-based builder protocol
pyproject.toml, server.json, glama.json	Bump to 0.22.3
docs/installation.md, docs/tools.md	Manifest workflow docs

Breaking changes

None. The manifest.json is created alongside the existing index database
and is backward-compatible. Existing indexes continue to work, but a
reindex (fw-context index --force) is required to get manifest-based
staleness detection and corrected file paths.

Upgrade instructions

pip install --upgrade fw-context-mcp
fw-context index --force   # run in each project root