Fixes#28 - Python site-packages directories (e.g.
audio_tools/python/Lib/site-packages/) were not excluded by default,
causing massive index bloat and FOREIGN KEY failures when indexing
large libraries like tensorflow. The FK crash itself was already fixed
via INSERT OR IGNORE, but excluding these directories prevents the
bloat in the first place.
- Remove getNodesByIds, getNodesByKinds (zero callers)
- Remove getFileHashMap, getFileSyncMap (zero callers)
- Remove getDynamicStmt cache (only used by removed batch methods)
- Revert getStaleFiles to simple implementation (zero callers, no need to optimize)
- Remove intent field from SearchOptions (never read in search logic)
- extraction/index.ts: use picomatch with static import (replacing
dynamic require) and keep normalizePath for other call sites
- utils.ts: keep normalizePath from main, take PR's PID-based FileLock
Both functions have zero callers — dead code on arrival. Remove them
and their tests (9 tests) to keep the module focused on what's
actually used: search term extraction, path relevance scoring, and
kind bonuses.
- Remove extractFunctionVariable() and its dispatch (already handled by extractVariable)
- Remove dead getGrammar() export (zero callers)
- Deduplicate indexFile by delegating to indexFileWithContent
- Remove redundant arrow function variable extraction tests (covered by existing suite)
- Create file-kind nodes for each parsed source file
- Add isInsideClassLikeNode() for method vs function detection
- Extract arrow functions and function expressions from variable declarators
- Batch file I/O with FILE_IO_BATCH_SIZE=10 using Promise.all
- Add symlink cycle detection with visitedDirs Set in scanDirectory
- Add lazy grammar loading with exported getGrammar() function
- Add indexFileWithContent() for pre-read content processing
- Add tests for file nodes and arrow function extraction
- Add provenance column on edges for tracking how edges were created
- Add project_metadata table for version/provenance tracking
- Make unresolved_refs file_path/language NOT NULL with defaults
- Add composite indexes for unresolved_refs and edges.provenance
- Update v2 migration to handle all new schema additions
- Record schema version on initialize to prevent re-migration
- Add dynamic prepared statement cache (getDynamicStmt) for varying SQL
- Add batch methods: getNodesByIds, getNodesByKinds, getFileHashMap, getFileSyncMap
- Add project metadata methods: getMetadata, setMetadata, getAllMetadata
- Optimize getStats to use single aggregate query
- Optimize getStaleFiles to use temporary table JOIN
- Add provenance parameter to getOutgoingEdges
- Add intent field to SearchOptions type
- Add validateProjectPath() to reject sensitive system directories
- Add isPathWithinRoot/isPathWithinRootReal for symlink-aware path checks
- Replace hand-rolled glob-to-regex with picomatch to prevent ReDoS
- Add isSafeRegex() to reject custom patterns with nested quantifiers
- Replace FileLock with PID-tracking version that detects stale locks
- Add symlink detection in removeDirectory/listDirectoryContents
- Add subdirectory name validation in ensureSubdirectory
- Add atomicWriteFileSync and corrupted file backup in config-writer
- Add MCP input validation (validateString) for all tool handlers
- Fix CLAUDE.md section replacement to handle ### subsections correctly
Normalize paths to forward slashes in matchesGlob() and scanDirectory()
so glob exclude patterns work on Windows. Add getGitIgnoredDirectories()
using git ls-files to skip .gitignore'd directories during indexing.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
All grammar packages now have compatible peer deps with tree-sitter 0.21.x,
resulting in zero warnings during npm install. Downgraded grammars:
c 0.24.1→0.23.2, php 0.24.2→0.23.11, python 0.23.6→0.23.4,
rust 0.24.0→0.23.1, swift 0.7.1→0.6.0.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reduces peer dependency warnings during install by upgrading grammars that
have newer versions accepting ^0.22.x: c 0.23.4→0.24.1, php 0.23.11→0.24.2,
rust 0.23.2→0.24.0. Python 0.23.6 and swift 0.7.1 already compatible.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
tree-sitter-kotlin doesn't ship prebuilt binaries for win32-x64, causing
npm install to fail on Windows without Visual Studio. All grammars are now
optional since the runtime already handles missing parsers gracefully.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add 'svelte' to Language type, DEFAULT_CONFIG includes, grammars, and config validation
- Add SvelteExtractor that extracts <script> blocks and delegates to TS/JS TreeSitterExtractor
- Add Svelte framework resolver for runes ($state, $derived, $effect, etc.), store auto-subscriptions, SvelteKit module aliases ($app/*, $env/*, $lib/*), and SvelteKit route detection
- Update README to list Svelte and Dart in supported languages
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
PostToolUse(Edit|Write) marks the project dirty via .codegraph/.dirty,
and Stop syncs only if dirty — batching all edits into one sync per
Claude response. The installer now writes these hooks to settings.json.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Node insertion used plain INSERT which crashes on duplicate IDs.
In large C/C++ projects, tree-sitter can produce duplicate nodes for
the same symbol (e.g. typedef struct where both struct_specifier and
type_definition resolve to the same name/kind/line, or multiple
anonymous constructs on the same line).
- Change nodes INSERT to INSERT OR REPLACE (idempotent, same data)
- Change edges INSERT to INSERT OR IGNORE (skip duplicate edges)
The node ID is sha256(filePath:kind:name:line) which already uses full
relative paths, so cross-directory collisions are not the issue.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
sqlite-vss fails to compile on Windows — moving it to optional lets
install succeed while the code already falls back to brute-force
vector search. tree-sitter-liquid is removed entirely as it has ABI
incompatibility with tree-sitter 0.22+ and Liquid is handled by the
built-in regex extractor.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Covers arrow function extraction, best-candidate resolution, graph
traversal direction fix, MCP symbol disambiguation, output truncation,
CLI uninit command, and more. Tests requiring better-sqlite3 native
bindings are conditionally skipped.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add findSymbol() helper that prefers exact name matches and notes
alternatives when multiple symbols share the same name
- Add output truncation (15K char cap) to prevent context window bloat
- Apply to callers, callees, impact, node, search, and files tools
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Exposes the existing uninitialize() method via `codegraph uninit [path]`.
Includes confirmation prompt (skippable with --force) before deleting
the .codegraph/ directory.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Fix arrow function extraction: explicitly call extractFunction() for
arrow functions/function expressions in variable declarations instead
of silently skipping them (all 6 arrow function tests now pass)
- Best-candidate resolution: collect candidates from all strategies and
return highest confidence match instead of first match
- Fix graph traversal 'both' direction: correctly determine next node
for mixed incoming/outgoing edges in BFS and DFS
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- SQLite performance pragmas: synchronous=NORMAL, 64MB cache,
memory temp store, 256MB mmap (safe with WAL mode)
- Batch insert for unresolved refs: single transaction instead of
N individual inserts per file
- Symbol caching (warmCaches): pre-load all nodes into memory maps
before resolution, eliminating repeated SQLite queries per ref
- Async file I/O: fs.stat/readFile in indexFile() are now non-blocking
- Denormalize filePath/language onto UnresolvedReference: avoids N
node lookups during resolution, with schema migration v2
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Fix Float32Array embedder bug: was creating zero-filled array instead
of copying data from TypedArray-like objects
- Fix VSS search query: use subquery pattern so LIMIT applies before JOIN
- Pin tree-sitter versions: remove caret ranges for ABI stability, add
overrides to lock tree-sitter core at 0.22.4
- Lazy grammar loading: load native bindings on first use per language
instead of all at startup, so one missing grammar doesn't affect others
- Remove stale src/extraction/queries copy from copy-assets script
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implements security improvements inspired by PR #16 (credit: MO2k4):
- Add validatePathWithinRoot() to prevent path traversal attacks in
extraction and context building
- Clamp MCP tool inputs (limit, depth, maxDepth) to sane ranges
- Use atomic writes (temp file + rename) for config saves
- Add symlink cycle detection in directory scanning to prevent infinite loops
- Replace all JSON.parse calls in db/queries.ts with safeJsonParse fallbacks
to handle corrupted database metadata gracefully
- Add cross-process FileLock for DB write operations (indexAll, indexFiles,
sync) to prevent concurrent writes from CLI, MCP server, and git hooks
- Remove unused path import from context/index.ts
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Adds support for Dart and Liquid languages with tree-sitter parsing.
Improves accuracy of code symbol extraction for existing languages.
Indexes project files to enhance code navigation features.
Migrates build system to facilitate code contributions.
Removes git hook functionality.
Integrates Sentry for error tracking and reporting.
Enhances project initialization and configuration loading.
Extend extraction to index two additional categories of symbols
that were previously invisible:
1. Type aliases (e.g. `export type X = ...` in TypeScript,
`type X` in Go, `type X = ...` in Rust, `typealias X` in Swift,
`type_alias` in Kotlin). Adds `typeAliasTypes` to the
LanguageExtractor interface with values for all 13 languages.
2. Exported variable declarations that aren't functions, including:
- Zustand stores: `export const useX = create(...)`
- XState machines: `export const xMachine = createMachine(...)`
- Zod schemas: `export const schema = z.object(...)`
- Config objects: `export const config = { ... }`
- Constants: `export const MAX = 3`
- Arrays: `export const NAMES = [...] as const`
The extractExportedVariables() method is called when visiting
export_statement nodes. It skips variable_declarator values that
are already handled by functionTypes (arrow_function,
function_expression) to avoid duplicate extraction.
Adds 11 new test cases (59 total extraction tests, 215 total).
Tested on production monorepo: nodes increased from 958 to 1,172
(+22%), with 109 new variable nodes and 105 new type_alias nodes.
Only 4 files remain at 0 nodes — all are re-export barrels or
ambient declaration files with no extractable symbols.
Arrow functions and function expressions assigned to variables
(e.g. `export const useAuth = () => { ... }`) were not being indexed
because the arrow_function AST node has no `name` field — the name
lives on the parent variable_declarator node.
Additionally, `isExported()` for TypeScript and JavaScript extractors
only checked 10 characters back from the node's start position, which
missed `export` for deeply nested nodes like arrow functions inside
variable declarations inside export statements.
Changes:
- extractFunction(): When an arrow_function or function_expression
resolves to '<anonymous>', look up the parent variable_declarator
for the name before skipping.
- isExported() (TS + JS): Walk the parent chain to find an
export_statement ancestor instead of substring matching.
- Add 6 test cases covering arrow function exports, function
expression exports, non-exported arrow functions, anonymous
arrow functions, multiple exports, and JavaScript files.
Tested on a real monorepo (238 files): node count increased from
779 to 958 (+23%), with 94 new nodes in packages/ that previously
had 0 coverage.
Olaf Monien
Colby McHenry
Martin Oehlert
Tanner Balluff