@colbymchenry/codegraph 0.2.9 → 0.5.0

package/dist/db/schema.sql

@@ -1,149 +1,163 @@
--- CodeGraph SQLite Schema
--- Version 1
-
--- Schema version tracking
-CREATE TABLE IF NOT EXISTS schema_versions (
-    version INTEGER PRIMARY KEY,
-    applied_at INTEGER NOT NULL,
-    description TEXT
-);
-
--- Insert initial version
-INSERT INTO schema_versions (version, applied_at, description)
-VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
-
--- =============================================================================
--- Core Tables
--- =============================================================================
-
--- Nodes: Code symbols (functions, classes, variables, etc.)
-CREATE TABLE IF NOT EXISTS nodes (
-    id TEXT PRIMARY KEY,
-    kind TEXT NOT NULL,
-    name TEXT NOT NULL,
-    qualified_name TEXT NOT NULL,
-    file_path TEXT NOT NULL,
-    language TEXT NOT NULL,
-    start_line INTEGER NOT NULL,
-    end_line INTEGER NOT NULL,
-    start_column INTEGER NOT NULL,
-    end_column INTEGER NOT NULL,
-    docstring TEXT,
-    signature TEXT,
-    visibility TEXT,
-    is_exported INTEGER DEFAULT 0,
-    is_async INTEGER DEFAULT 0,
-    is_static INTEGER DEFAULT 0,
-    is_abstract INTEGER DEFAULT 0,
-    decorators TEXT, -- JSON array
-    type_parameters TEXT, -- JSON array
-    updated_at INTEGER NOT NULL
-);
-
--- Edges: Relationships between nodes
-CREATE TABLE IF NOT EXISTS edges (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    source TEXT NOT NULL,
-    target TEXT NOT NULL,
-    kind TEXT NOT NULL,
-    metadata TEXT, -- JSON object
-    line INTEGER,
-    col INTEGER,
-    FOREIGN KEY (source) REFERENCES nodes(id) ON DELETE CASCADE,
-    FOREIGN KEY (target) REFERENCES nodes(id) ON DELETE CASCADE
-);
-
--- Files: Tracked source files
-CREATE TABLE IF NOT EXISTS files (
-    path TEXT PRIMARY KEY,
-    content_hash TEXT NOT NULL,
-    language TEXT NOT NULL,
-    size INTEGER NOT NULL,
-    modified_at INTEGER NOT NULL,
-    indexed_at INTEGER NOT NULL,
-    node_count INTEGER DEFAULT 0,
-    errors TEXT -- JSON array
-);
-
--- Unresolved References: References that need resolution after full indexing
-CREATE TABLE IF NOT EXISTS unresolved_refs (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    from_node_id TEXT NOT NULL,
-    reference_name TEXT NOT NULL,
-    reference_kind TEXT NOT NULL,
-    line INTEGER NOT NULL,
-    col INTEGER NOT NULL,
-    candidates TEXT, -- JSON array
-    FOREIGN KEY (from_node_id) REFERENCES nodes(id) ON DELETE CASCADE
-);
-
--- =============================================================================
--- Indexes for Query Performance
--- =============================================================================
-
--- Node indexes
-CREATE INDEX IF NOT EXISTS idx_nodes_kind ON nodes(kind);
-CREATE INDEX IF NOT EXISTS idx_nodes_name ON nodes(name);
-CREATE INDEX IF NOT EXISTS idx_nodes_qualified_name ON nodes(qualified_name);
-CREATE INDEX IF NOT EXISTS idx_nodes_file_path ON nodes(file_path);
-CREATE INDEX IF NOT EXISTS idx_nodes_language ON nodes(language);
-CREATE INDEX IF NOT EXISTS idx_nodes_file_line ON nodes(file_path, start_line);
-
--- Full-text search index on node names and docstrings
-CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(
-    id,
-    name,
-    qualified_name,
-    docstring,
-    content='nodes',
-    content_rowid='rowid'
-);
-
--- Triggers to keep FTS index in sync
-CREATE TRIGGER IF NOT EXISTS nodes_ai AFTER INSERT ON nodes BEGIN
-    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring)
-    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring);
-END;
-
-CREATE TRIGGER IF NOT EXISTS nodes_ad AFTER DELETE ON nodes BEGIN
-    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring)
-    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring);
-END;
-
-CREATE TRIGGER IF NOT EXISTS nodes_au AFTER UPDATE ON nodes BEGIN
-    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring)
-    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring);
-    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring)
-    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring);
-END;
-
--- Edge indexes
-CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source);
-CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target);
-CREATE INDEX IF NOT EXISTS idx_edges_kind ON edges(kind);
-CREATE INDEX IF NOT EXISTS idx_edges_source_kind ON edges(source, kind);
-CREATE INDEX IF NOT EXISTS idx_edges_target_kind ON edges(target, kind);
-
--- File indexes
-CREATE INDEX IF NOT EXISTS idx_files_language ON files(language);
-CREATE INDEX IF NOT EXISTS idx_files_modified_at ON files(modified_at);
-
--- Unresolved refs indexes
-CREATE INDEX IF NOT EXISTS idx_unresolved_from_node ON unresolved_refs(from_node_id);
-CREATE INDEX IF NOT EXISTS idx_unresolved_name ON unresolved_refs(reference_name);
-
--- =============================================================================
--- Vector Storage (for future semantic search)
--- =============================================================================
-
--- Vector embeddings for semantic search
--- Note: No foreign key constraint to allow standalone vector testing
--- The VectorManager handles node-vector relationship at the application level
-CREATE TABLE IF NOT EXISTS vectors (
-    node_id TEXT PRIMARY KEY,
-    embedding BLOB NOT NULL, -- Float32 array stored as blob
-    model TEXT NOT NULL, -- Model used to generate embedding
-    created_at INTEGER NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS idx_vectors_model ON vectors(model);
+-- CodeGraph SQLite Schema
+-- Version 1
+
+-- Schema version tracking
+CREATE TABLE IF NOT EXISTS schema_versions (
+    version INTEGER PRIMARY KEY,
+    applied_at INTEGER NOT NULL,
+    description TEXT
+);
+
+-- Insert initial version
+INSERT INTO schema_versions (version, applied_at, description)
+VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
+
+-- =============================================================================
+-- Core Tables
+-- =============================================================================
+
+-- Nodes: Code symbols (functions, classes, variables, etc.)
+CREATE TABLE IF NOT EXISTS nodes (
+    id TEXT PRIMARY KEY,
+    kind TEXT NOT NULL,
+    name TEXT NOT NULL,
+    qualified_name TEXT NOT NULL,
+    file_path TEXT NOT NULL,
+    language TEXT NOT NULL,
+    start_line INTEGER NOT NULL,
+    end_line INTEGER NOT NULL,
+    start_column INTEGER NOT NULL,
+    end_column INTEGER NOT NULL,
+    docstring TEXT,
+    signature TEXT,
+    visibility TEXT,
+    is_exported INTEGER DEFAULT 0,
+    is_async INTEGER DEFAULT 0,
+    is_static INTEGER DEFAULT 0,
+    is_abstract INTEGER DEFAULT 0,
+    decorators TEXT, -- JSON array
+    type_parameters TEXT, -- JSON array
+    updated_at INTEGER NOT NULL
+);
+
+-- Edges: Relationships between nodes
+CREATE TABLE IF NOT EXISTS edges (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    source TEXT NOT NULL,
+    target TEXT NOT NULL,
+    kind TEXT NOT NULL,
+    metadata TEXT, -- JSON object
+    line INTEGER,
+    col INTEGER,
+    provenance TEXT DEFAULT NULL,
+    FOREIGN KEY (source) REFERENCES nodes(id) ON DELETE CASCADE,
+    FOREIGN KEY (target) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+-- Files: Tracked source files
+CREATE TABLE IF NOT EXISTS files (
+    path TEXT PRIMARY KEY,
+    content_hash TEXT NOT NULL,
+    language TEXT NOT NULL,
+    size INTEGER NOT NULL,
+    modified_at INTEGER NOT NULL,
+    indexed_at INTEGER NOT NULL,
+    node_count INTEGER DEFAULT 0,
+    errors TEXT -- JSON array
+);
+
+-- Unresolved References: References that need resolution after full indexing
+CREATE TABLE IF NOT EXISTS unresolved_refs (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    from_node_id TEXT NOT NULL,
+    reference_name TEXT NOT NULL,
+    reference_kind TEXT NOT NULL,
+    line INTEGER NOT NULL,
+    col INTEGER NOT NULL,
+    candidates TEXT, -- JSON array
+    file_path TEXT NOT NULL DEFAULT '',
+    language TEXT NOT NULL DEFAULT 'unknown',
+    FOREIGN KEY (from_node_id) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+-- =============================================================================
+-- Indexes for Query Performance
+-- =============================================================================
+
+-- Node indexes
+CREATE INDEX IF NOT EXISTS idx_nodes_kind ON nodes(kind);
+CREATE INDEX IF NOT EXISTS idx_nodes_name ON nodes(name);
+CREATE INDEX IF NOT EXISTS idx_nodes_qualified_name ON nodes(qualified_name);
+CREATE INDEX IF NOT EXISTS idx_nodes_file_path ON nodes(file_path);
+CREATE INDEX IF NOT EXISTS idx_nodes_language ON nodes(language);
+CREATE INDEX IF NOT EXISTS idx_nodes_file_line ON nodes(file_path, start_line);
+
+-- Full-text search index on node names, docstrings, and signatures
+CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(
+    id,
+    name,
+    qualified_name,
+    docstring,
+    signature,
+    content='nodes',
+    content_rowid='rowid'
+);
+
+-- Triggers to keep FTS index in sync
+CREATE TRIGGER IF NOT EXISTS nodes_ai AFTER INSERT ON nodes BEGIN
+    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring, signature)
+    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring, NEW.signature);
+END;
+
+CREATE TRIGGER IF NOT EXISTS nodes_ad AFTER DELETE ON nodes BEGIN
+    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring, signature)
+    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring, OLD.signature);
+END;
+
+CREATE TRIGGER IF NOT EXISTS nodes_au AFTER UPDATE ON nodes BEGIN
+    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring, signature)
+    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring, OLD.signature);
+    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring, signature)
+    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring, NEW.signature);
+END;
+
+-- Edge indexes
+CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source);
+CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target);
+CREATE INDEX IF NOT EXISTS idx_edges_kind ON edges(kind);
+CREATE INDEX IF NOT EXISTS idx_edges_source_kind ON edges(source, kind);
+CREATE INDEX IF NOT EXISTS idx_edges_target_kind ON edges(target, kind);
+
+-- File indexes
+CREATE INDEX IF NOT EXISTS idx_files_language ON files(language);
+CREATE INDEX IF NOT EXISTS idx_files_modified_at ON files(modified_at);
+
+-- Unresolved refs indexes
+CREATE INDEX IF NOT EXISTS idx_unresolved_from_node ON unresolved_refs(from_node_id);
+CREATE INDEX IF NOT EXISTS idx_unresolved_name ON unresolved_refs(reference_name);
+CREATE INDEX IF NOT EXISTS idx_unresolved_file_path ON unresolved_refs(file_path);
+CREATE INDEX IF NOT EXISTS idx_unresolved_from_name ON unresolved_refs(from_node_id, reference_name);
+CREATE INDEX IF NOT EXISTS idx_edges_provenance ON edges(provenance);
+
+-- =============================================================================
+-- Vector Storage (for future semantic search)
+-- =============================================================================
+
+-- Vector embeddings for semantic search
+-- Note: No foreign key constraint to allow standalone vector testing
+-- The VectorManager handles node-vector relationship at the application level
+CREATE TABLE IF NOT EXISTS vectors (
+    node_id TEXT PRIMARY KEY,
+    embedding BLOB NOT NULL, -- Float32 array stored as blob
+    model TEXT NOT NULL, -- Model used to generate embedding
+    created_at INTEGER NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_vectors_model ON vectors(model);
+
+-- Project metadata for version/provenance tracking
+CREATE TABLE IF NOT EXISTS project_metadata (
+    key TEXT PRIMARY KEY,
+    value TEXT NOT NULL,
+    updated_at INTEGER NOT NULL
+);

package/dist/directory.d.ts

@@ -1,7 +1,7 @@
 /**
  * Directory Management
  *
- * Manages the .codegraph/ directory structure.
+ * Manages the .codegraph/ directory structure for CodeGraph data.
  */
 /**
  * CodeGraph directory name
@@ -13,10 +13,22 @@ export declare const CODEGRAPH_DIR = ".codegraph";
 export declare function getCodeGraphDir(projectRoot: string): string;
 /**
  * Check if a project has been initialized with CodeGraph
+ * Requires both .codegraph/ directory AND codegraph.db to exist
  */
 export declare function isInitialized(projectRoot: string): boolean;
+/**
+ * Find the nearest parent directory containing .codegraph/
+ *
+ * Walks up from the given path to find a CodeGraph-initialized project,
+ * similar to how git finds .git/ directories.
+ *
+ * @param startPath - Directory to start searching from
+ * @returns The project root containing .codegraph/, or null if not found
+ */
+export declare function findNearestCodeGraphRoot(startPath: string): string | null;
 /**
  * Create the .codegraph directory structure
+ * Note: Only throws if codegraph.db already exists, not just if .codegraph/ exists.
  */
 export declare function createDirectory(projectRoot: string): void;
 /**

package/dist/directory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"directory.d.ts","sourceRoot":"","sources":["../src/directory.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH;;GAEG;AACH,eAAO,MAAM,aAAa,eAAe,CAAC;AAE1C;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;GAEG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAG1D;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CA4BzD;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CASzD;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAyBnE;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CA0B5D;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAQlF;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG;IACtD,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAwBA"}
+{"version":3,"file":"directory.d.ts","sourceRoot":"","sources":["../src/directory.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH;;GAEG;AACH,eAAO,MAAM,aAAa,eAAe,CAAC;AAE1C;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;;GAGG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAQ1D;AAED;;;;;;;;GAQG;AACH,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAmBzE;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAoCzD;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAuBzD;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CA8BnE;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CA+B5D;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAYlF;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG;IACtD,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAwBA"}

package/dist/directory.js

@@ -2,7 +2,7 @@
 /**
  * Directory Management
  *
- * Manages the .codegraph/ directory structure.
+ * Manages the .codegraph/ directory structure for CodeGraph data.
  */
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
@@ -41,6 +41,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.CODEGRAPH_DIR = void 0;
 exports.getCodeGraphDir = getCodeGraphDir;
 exports.isInitialized = isInitialized;
+exports.findNearestCodeGraphRoot = findNearestCodeGraphRoot;
 exports.createDirectory = createDirectory;
 exports.removeDirectory = removeDirectory;
 exports.listDirectoryContents = listDirectoryContents;
@@ -61,38 +62,80 @@ function getCodeGraphDir(projectRoot) {
 }
 /**
  * Check if a project has been initialized with CodeGraph
+ * Requires both .codegraph/ directory AND codegraph.db to exist
  */
 function isInitialized(projectRoot) {
     const codegraphDir = getCodeGraphDir(projectRoot);
-    return fs.existsSync(codegraphDir) && fs.statSync(codegraphDir).isDirectory();
+    if (!fs.existsSync(codegraphDir) || !fs.statSync(codegraphDir).isDirectory()) {
+        return false;
+    }
+    // Must have codegraph.db, not just .codegraph folder
+    const dbPath = path.join(codegraphDir, 'codegraph.db');
+    return fs.existsSync(dbPath);
+}
+/**
+ * Find the nearest parent directory containing .codegraph/
+ *
+ * Walks up from the given path to find a CodeGraph-initialized project,
+ * similar to how git finds .git/ directories.
+ *
+ * @param startPath - Directory to start searching from
+ * @returns The project root containing .codegraph/, or null if not found
+ */
+function findNearestCodeGraphRoot(startPath) {
+    let current = path.resolve(startPath);
+    const root = path.parse(current).root;
+    while (current !== root) {
+        if (isInitialized(current)) {
+            return current;
+        }
+        const parent = path.dirname(current);
+        if (parent === current)
+            break; // Reached filesystem root
+        current = parent;
+    }
+    // Check root as well
+    if (isInitialized(current)) {
+        return current;
+    }
+    return null;
 }
 /**
  * Create the .codegraph directory structure
+ * Note: Only throws if codegraph.db already exists, not just if .codegraph/ exists.
  */
 function createDirectory(projectRoot) {
     const codegraphDir = getCodeGraphDir(projectRoot);
-    if (fs.existsSync(codegraphDir)) {
+    const dbPath = path.join(codegraphDir, 'codegraph.db');
+    // Only throw if CodeGraph is actually initialized (db exists)
+    // .codegraph/ folder alone is fine
+    if (fs.existsSync(dbPath)) {
         throw new Error(`CodeGraph already initialized in ${projectRoot}`);
     }
-    // Create main directory
+    // Create main directory (if it doesn't exist)
     fs.mkdirSync(codegraphDir, { recursive: true });
-    // Create .gitignore inside .codegraph
+    // Create .gitignore inside .codegraph (if it doesn't exist)
     const gitignorePath = path.join(codegraphDir, '.gitignore');
-    const gitignoreContent = `# CodeGraph data files
-# These are local to each machine and should not be committed
-
-# Database
-*.db
-*.db-wal
-*.db-shm
-
-# Cache
-cache/
-
-# Logs
-*.log
+    if (!fs.existsSync(gitignorePath)) {
+        const gitignoreContent = `# CodeGraph data files
+# These are local to each machine and should not be committed
+
+# Database
+*.db
+*.db-wal
+*.db-shm
+
+# Cache
+cache/
+
+# Logs
+*.log
+
+# Hook markers
+.dirty
 `;
-    fs.writeFileSync(gitignorePath, gitignoreContent, 'utf-8');
+        fs.writeFileSync(gitignorePath, gitignoreContent, 'utf-8');
+    }
 }
 /**
  * Remove the .codegraph directory
@@ -102,6 +145,18 @@ function removeDirectory(projectRoot) {
     if (!fs.existsSync(codegraphDir)) {
         return;
     }
+    // Verify .codegraph is a real directory, not a symlink pointing elsewhere
+    const lstat = fs.lstatSync(codegraphDir);
+    if (lstat.isSymbolicLink()) {
+        // Only remove the symlink itself, never follow it for recursive delete
+        fs.unlinkSync(codegraphDir);
+        return;
+    }
+    if (!lstat.isDirectory()) {
+        // Not a directory - remove the single file
+        fs.unlinkSync(codegraphDir);
+        return;
+    }
     // Recursively remove directory
     fs.rmSync(codegraphDir, { recursive: true, force: true });
 }
@@ -118,6 +173,10 @@ function listDirectoryContents(projectRoot) {
         const entries = fs.readdirSync(dir, { withFileTypes: true });
         for (const entry of entries) {
             const relativePath = prefix ? `${prefix}/${entry.name}` : entry.name;
+            // Skip symlinks to prevent following links outside .codegraph
+            if (entry.isSymbolicLink()) {
+                continue;
+            }
             if (entry.isDirectory()) {
                 walkDir(path.join(dir, entry.name), relativePath);
             }
@@ -141,6 +200,10 @@ function getDirectorySize(projectRoot) {
     function walkDir(dir) {
         const entries = fs.readdirSync(dir, { withFileTypes: true });
         for (const entry of entries) {
+            // Skip symlinks to prevent following links outside .codegraph
+            if (entry.isSymbolicLink()) {
+                continue;
+            }
             const fullPath = path.join(dir, entry.name);
             if (entry.isDirectory()) {
                 walkDir(fullPath);
@@ -158,6 +221,9 @@ function getDirectorySize(projectRoot) {
  * Ensure a subdirectory exists within .codegraph
  */
 function ensureSubdirectory(projectRoot, subdirName) {
+    if (subdirName.includes('..') || subdirName.includes(path.sep) || subdirName.includes('/')) {
+        throw new Error(`Invalid subdirectory name: ${subdirName}`);
+    }
     const subdirPath = path.join(getCodeGraphDir(projectRoot), subdirName);
     if (!fs.existsSync(subdirPath)) {
         fs.mkdirSync(subdirPath, { recursive: true });

package/dist/directory.js.map

@@ -1 +1 @@
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+{"version":3,"file":"directory.js","sourceRoot":"","sources":["../src/directory.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAaH,0CAEC;AAMD,sCAQC;AAWD,4DAmBC;AAMD,0CAoCC;AAKD,0CAuBC;AAKD,sDA8BC;AAKD,4CA+BC;AAKD,gDAYC;AAKD,8CA2BC;AAvPD,uCAAyB;AACzB,2CAA6B;AAE7B;;GAEG;AACU,QAAA,aAAa,GAAG,YAAY,CAAC;AAE1C;;GAEG;AACH,SAAgB,eAAe,CAAC,WAAmB;IACjD,OAAO,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,qBAAa,CAAC,CAAC;AAC/C,CAAC;AAED;;;GAGG;AACH,SAAgB,aAAa,CAAC,WAAmB;IAC/C,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAClD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC;QAC7E,OAAO,KAAK,CAAC;IACf,CAAC;IACD,qDAAqD;IACrD,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,cAAc,CAAC,CAAC;IACvD,OAAO,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC;AAC/B,CAAC;AAED;;;;;;;;GAQG;AACH,SAAgB,wBAAwB,CAAC,SAAiB;IACxD,IAAI,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IACtC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC;IAEtC,OAAO,OAAO,KAAK,IAAI,EAAE,CAAC;QACxB,IAAI,aAAa,CAAC,OAAO,CAAC,EAAE,CAAC;YAC3B,OAAO,OAAO,CAAC;QACjB,CAAC;QACD,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QACrC,IAAI,MAAM,KAAK,OAAO;YAAE,MAAM,CAAC,0BAA0B;QACzD,OAAO,GAAG,MAAM,CAAC;IACnB,CAAC;IAED,qBAAqB;IACrB,IAAI,aAAa,CAAC,OAAO,CAAC,EAAE,CAAC;QAC3B,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;GAGG;AACH,SAAgB,eAAe,CAAC,WAAmB;IACjD,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAClD,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,cAAc,CAAC,CAAC;IAEvD,8DAA8D;IAC9D,mCAAmC;IACnC,IAAI,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;QAC1B,MAAM,IAAI,KAAK,CAAC,oCAAoC,WAAW,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,8CAA8C;IAC9C,EAAE,CAAC,SAAS,CAAC,YAAY,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAEhD,4DAA4D;IAC5D,MAAM,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC,CAAC;IAC5D,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;QAClC,MAAM,gBAAgB,GAAG;;;;;;;;;;;;;;;;CAgB5B,CAAC;QAEE,EAAE,CAAC,aAAa,CAAC,aAAa,EAAE,gBAAgB,EAAE,OAAO,CAAC,CAAC;IAC7D,CAAC;AACH,CAAC;AAED;;GAEG;AACH,SAAgB,eAAe,CAAC,WAAmB;IACjD,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAElD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,OAAO;IACT,CAAC;IAED,0EAA0E;IAC1E,MAAM,KAAK,GAAG,EAAE,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC;IACzC,IAAI,KAAK,CAAC,cAAc,EAAE,EAAE,CAAC;QAC3B,uEAAuE;QACvE,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,CAAC;QAC5B,OAAO;IACT,CAAC;IAED,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;QACzB,2CAA2C;QAC3C,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,CAAC;QAC5B,OAAO;IACT,CAAC;IAED,+BAA+B;IAC/B,EAAE,CAAC,MAAM,CAAC,YAAY,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;AAC5D,CAAC;AAED;;GAEG;AACH,SAAgB,qBAAqB,CAAC,WAAmB;IACvD,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAElD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,MAAM,KAAK,GAAa,EAAE,CAAC;IAE3B,SAAS,OAAO,CAAC,GAAW,EAAE,SAAiB,EAAE;QAC/C,MAAM,OAAO,GAAG,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;QAE7D,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;YAC5B,MAAM,YAAY,GAAG,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC;YAErE,8DAA8D;YAC9D,IAAI,KAAK,CAAC,cAAc,EAAE,EAAE,CAAC;gBAC3B,SAAS;YACX,CAAC;YAED,IAAI,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;gBACxB,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,EAAE,YAAY,CAAC,CAAC;YACpD,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;YAC3B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,CAAC,YAAY,CAAC,CAAC;IACtB,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;GAEG;AACH,SAAgB,gBAAgB,CAAC,WAAmB;IAClD,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAElD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,OAAO,CAAC,CAAC;IACX,CAAC;IAED,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,SAAS,OAAO,CAAC,GAAW;QAC1B,MAAM,OAAO,GAAG,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;QAE7D,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;YAC5B,8DAA8D;YAC9D,IAAI,KAAK,CAAC,cAAc,EAAE,EAAE,CAAC;gBAC3B,SAAS;YACX,CAAC;YAED,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;YAE5C,IAAI,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC;gBACxB,OAAO,CAAC,QAAQ,CAAC,CAAC;YACpB,CAAC;iBAAM,CAAC;gBACN,MAAM,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;gBACpC,SAAS,IAAI,KAAK,CAAC,IAAI,CAAC;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,CAAC,YAAY,CAAC,CAAC;IACtB,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;GAEG;AACH,SAAgB,kBAAkB,CAAC,WAAmB,EAAE,UAAkB;IACxE,IAAI,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QAC3F,MAAM,IAAI,KAAK,CAAC,8BAA8B,UAAU,EAAE,CAAC,CAAC;IAC9D,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,eAAe,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,CAAC;IAEvE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,EAAE,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAChD,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC;AAED;;GAEG;AACH,SAAgB,iBAAiB,CAAC,WAAmB;IAInD,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,YAAY,GAAG,eAAe,CAAC,WAAW,CAAC,CAAC;IAElD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,MAAM,CAAC,IAAI,CAAC,oCAAoC,CAAC,CAAC;QAClD,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAClC,CAAC;IAED,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC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package/dist/errors.d.ts

@@ -130,7 +130,7 @@ export declare function logDebug(message: string, context?: Record<string, unkno
  */
 export declare function logWarn(message: string, context?: Record<string, unknown>): void;
 /**
- * Log an error message
+ * Log an error message (also sends to Sentry if initialized)
  */
 export declare function logError(message: string, context?: Record<string, unknown>): void;
 //# sourceMappingURL=errors.d.ts.map

package/dist/errors.d.ts.map

@@ -1 +1 @@
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package/dist/errors.js

@@ -211,9 +211,15 @@ function logWarn(message, context) {
     currentLogger.warn(message, context);
 }
 /**
- * Log an error message
+ * Log an error message (also sends to Sentry if initialized)
  */
 function logError(message, context) {
     currentLogger.error(message, context);
+    // Lazy import to avoid circular deps
+    try {
+        const { captureMessage } = require('./sentry');
+        captureMessage(message, context);
+    }
+    catch { }
 }
 //# sourceMappingURL=errors.js.map

package/dist/errors.js.map

@@ -1 +1 @@
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package/dist/extraction/grammars.d.ts

@@ -1,7 +1,8 @@
 /**
  * Grammar Loading and Caching
  *
- * Manages tree-sitter language grammars.
+ * Uses lazy per-language loading so one missing native grammar does not
+ * break extraction for all other languages.
  */
 import Parser from 'tree-sitter';
 import { Language } from '../types';
@@ -18,17 +19,21 @@ export declare function getParser(language: Language): Parser | null;
  */
 export declare function detectLanguage(filePath: string): Language;
 /**
- * Check if a language is supported
+ * Check if a language is supported by currently available parsers.
  */
 export declare function isLanguageSupported(language: Language): boolean;
 /**
- * Get all supported languages
+ * Get all currently supported languages.
  */
 export declare function getSupportedLanguages(): Language[];
 /**
- * Clear the parser cache (useful for testing)
+ * Clear parser/grammar caches (useful for testing)
  */
 export declare function clearParserCache(): void;
+/**
+ * Report grammars that failed to load.
+ */
+export declare function getUnavailableGrammarErrors(): Partial<Record<Language, string>>;
 /**
  * Get language display name
  */