@quolu/lattice 0.1.0

package/sensor/dist/index.js

@@ -0,0 +1,1646 @@
+"use strict";
+/**
+ * CodeGraph
+ *
+ * A local-first code intelligence system that builds a semantic
+ * knowledge graph from any codebase.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CodeGraph = exports.MCPServer = exports.LockUnavailableError = exports.FileWatcher = exports.MemoryMonitor = exports.throttle = exports.debounce = exports.processInBatches = exports.FileLock = exports.Mutex = exports.defaultLogger = exports.silentLogger = exports.getLogger = exports.setLogger = exports.ConfigError = exports.VectorError = exports.SearchError = exports.DatabaseError = exports.ParseError = exports.FileError = exports.CodeGraphError = exports.loadAllGrammars = exports.loadGrammarsForLanguages = exports.initGrammars = exports.getSupportedLanguages = exports.isGrammarLoaded = exports.isLanguageSupported = exports.detectLanguage = exports.CODEGRAPH_DIR = exports.findNearestCodeGraphRoot = exports.isInitialized = exports.getCodeGraphDir = exports.QueryBuilder = exports.DatabaseConnection = exports.getDatabasePath = void 0;
+const path = __importStar(require("path"));
+const db_1 = require("./db");
+const wal_valve_1 = require("./db/wal-valve");
+const queries_1 = require("./db/queries");
+const directory_1 = require("./directory");
+const extraction_1 = require("./extraction");
+const resolution_1 = require("./resolution");
+const graph_1 = require("./graph");
+const context_1 = require("./context");
+const utils_1 = require("./utils");
+const sync_1 = require("./sync");
+const extraction_version_1 = require("./extraction/extraction-version");
+const directory_2 = require("./directory");
+const query_utils_1 = require("./search/query-utils");
+const version_1 = require("./mcp/version");
+const identifier_segments_1 = require("./search/identifier-segments");
+const cooperative_yield_1 = require("./resolution/cooperative-yield");
+const resolver_pool_1 = require("./resolution/resolver-pool");
+// Re-export types for consumers
+__exportStar(require("./types"), exports);
+// Storage building blocks for embedded/SDK consumers that drive the graph
+// directly (open a DB, run prepared queries) rather than through the CodeGraph
+// facade. Exposed from the package entry so they no longer require deep imports
+// into dist/ (issue #354).
+var db_2 = require("./db");
+Object.defineProperty(exports, "getDatabasePath", { enumerable: true, get: function () { return db_2.getDatabasePath; } });
+Object.defineProperty(exports, "DatabaseConnection", { enumerable: true, get: function () { return db_2.DatabaseConnection; } });
+var queries_2 = require("./db/queries");
+Object.defineProperty(exports, "QueryBuilder", { enumerable: true, get: function () { return queries_2.QueryBuilder; } });
+var directory_3 = require("./directory");
+Object.defineProperty(exports, "getCodeGraphDir", { enumerable: true, get: function () { return directory_3.getCodeGraphDir; } });
+Object.defineProperty(exports, "isInitialized", { enumerable: true, get: function () { return directory_3.isInitialized; } });
+Object.defineProperty(exports, "findNearestCodeGraphRoot", { enumerable: true, get: function () { return directory_3.findNearestCodeGraphRoot; } });
+Object.defineProperty(exports, "CODEGRAPH_DIR", { enumerable: true, get: function () { return directory_3.CODEGRAPH_DIR; } });
+var extraction_2 = require("./extraction");
+Object.defineProperty(exports, "detectLanguage", { enumerable: true, get: function () { return extraction_2.detectLanguage; } });
+Object.defineProperty(exports, "isLanguageSupported", { enumerable: true, get: function () { return extraction_2.isLanguageSupported; } });
+Object.defineProperty(exports, "isGrammarLoaded", { enumerable: true, get: function () { return extraction_2.isGrammarLoaded; } });
+Object.defineProperty(exports, "getSupportedLanguages", { enumerable: true, get: function () { return extraction_2.getSupportedLanguages; } });
+Object.defineProperty(exports, "initGrammars", { enumerable: true, get: function () { return extraction_2.initGrammars; } });
+Object.defineProperty(exports, "loadGrammarsForLanguages", { enumerable: true, get: function () { return extraction_2.loadGrammarsForLanguages; } });
+Object.defineProperty(exports, "loadAllGrammars", { enumerable: true, get: function () { return extraction_2.loadAllGrammars; } });
+var errors_1 = require("./errors");
+Object.defineProperty(exports, "CodeGraphError", { enumerable: true, get: function () { return errors_1.CodeGraphError; } });
+Object.defineProperty(exports, "FileError", { enumerable: true, get: function () { return errors_1.FileError; } });
+Object.defineProperty(exports, "ParseError", { enumerable: true, get: function () { return errors_1.ParseError; } });
+Object.defineProperty(exports, "DatabaseError", { enumerable: true, get: function () { return errors_1.DatabaseError; } });
+Object.defineProperty(exports, "SearchError", { enumerable: true, get: function () { return errors_1.SearchError; } });
+Object.defineProperty(exports, "VectorError", { enumerable: true, get: function () { return errors_1.VectorError; } });
+Object.defineProperty(exports, "ConfigError", { enumerable: true, get: function () { return errors_1.ConfigError; } });
+Object.defineProperty(exports, "setLogger", { enumerable: true, get: function () { return errors_1.setLogger; } });
+Object.defineProperty(exports, "getLogger", { enumerable: true, get: function () { return errors_1.getLogger; } });
+Object.defineProperty(exports, "silentLogger", { enumerable: true, get: function () { return errors_1.silentLogger; } });
+Object.defineProperty(exports, "defaultLogger", { enumerable: true, get: function () { return errors_1.defaultLogger; } });
+var utils_2 = require("./utils");
+Object.defineProperty(exports, "Mutex", { enumerable: true, get: function () { return utils_2.Mutex; } });
+Object.defineProperty(exports, "FileLock", { enumerable: true, get: function () { return utils_2.FileLock; } });
+Object.defineProperty(exports, "processInBatches", { enumerable: true, get: function () { return utils_2.processInBatches; } });
+Object.defineProperty(exports, "debounce", { enumerable: true, get: function () { return utils_2.debounce; } });
+Object.defineProperty(exports, "throttle", { enumerable: true, get: function () { return utils_2.throttle; } });
+Object.defineProperty(exports, "MemoryMonitor", { enumerable: true, get: function () { return utils_2.MemoryMonitor; } });
+var sync_2 = require("./sync");
+Object.defineProperty(exports, "FileWatcher", { enumerable: true, get: function () { return sync_2.FileWatcher; } });
+Object.defineProperty(exports, "LockUnavailableError", { enumerable: true, get: function () { return sync_2.LockUnavailableError; } });
+var mcp_1 = require("./mcp");
+Object.defineProperty(exports, "MCPServer", { enumerable: true, get: function () { return mcp_1.MCPServer; } });
+/**
+ * Main CodeGraph class
+ *
+ * Provides the primary interface for interacting with the code knowledge graph.
+ */
+class CodeGraph {
+    db;
+    queries;
+    projectRoot;
+    // Assigned via wireLayers() from the constructor (and again on reopen) — the
+    // `!` tells TS these are definitely set even though the assignment is one
+    // method call away from the constructor body.
+    orchestrator;
+    resolver;
+    graphManager;
+    traverser;
+    contextBuilder;
+    // Mutex for preventing concurrent indexing operations (in-process)
+    indexMutex = new utils_1.Mutex();
+    // File lock for preventing concurrent writes across processes (CLI, MCP, git hooks)
+    fileLock;
+    // File watcher for auto-sync on file changes
+    watcher = null;
+    constructor(db, queries, projectRoot) {
+        this.db = db;
+        this.queries = queries;
+        this.projectRoot = projectRoot;
+        this.fileLock = new utils_1.FileLock(path.join((0, directory_2.getCodeGraphDir)(projectRoot), 'codegraph.lock'));
+        this.wireLayers();
+    }
+    /**
+     * (Re)build the query/extraction/graph layers over the current `this.queries`
+     * (which wraps `this.db`). Factored out of the constructor so `reopenIfReplaced`
+     * can rebuild them against a fresh connection without duplicating the wiring.
+     * The path-based `fileLock` is independent of the DB handle, so it stays put.
+     */
+    wireLayers() {
+        // Down-weight the project name as a query term in search ranking — it names
+        // the whole repo, not a symbol, so it has no discriminative value (#720).
+        try {
+            this.queries.setProjectNameTokens((0, query_utils_1.deriveProjectNameTokens)(this.projectRoot));
+        }
+        catch {
+            // Best-effort: ranking still works without it.
+        }
+        this.orchestrator = new extraction_1.ExtractionOrchestrator(this.projectRoot, this.queries);
+        this.resolver = (0, resolution_1.createResolver)(this.projectRoot, this.queries);
+        this.graphManager = new graph_1.GraphQueryManager(this.queries);
+        this.traverser = new graph_1.GraphTraverser(this.queries);
+        this.contextBuilder = (0, context_1.createContextBuilder)(this.projectRoot, this.queries, this.traverser);
+    }
+    /**
+     * Heal a stale database handle in place. If `.codegraph/` was removed and
+     * recreated at the SAME path while this instance held the DB open — a git
+     * worktree removed and re-added, or `rm -rf .codegraph` + `codegraph init` —
+     * our open fd points at the now-unlinked inode and can never see the new
+     * index, so every query returns the pre-removal snapshot until the process
+     * restarts (#925). When that's detected, open the live file at the same path,
+     * rebuild the query layers, and swap them IN PLACE, so every holder of this
+     * instance (the MCP daemon's default project, cached projectPath connections)
+     * heals without a restart. Returns true iff it reopened.
+     *
+     * POSIX-only in practice: `isReplacedOnDisk` never fires on Windows (an open
+     * file can't be unlinked there, and st_ino is unreliable).
+     */
+    reopenIfReplaced() {
+        if (!this.db.isReplacedOnDisk())
+            return false;
+        const dbPath = this.db.getPath();
+        // Open the live file FIRST — if that throws (e.g. mid-recreate), the old
+        // handle stays in place and the caller retries on the next query, rather
+        // than leaving this instance with no connection at all.
+        const fresh = db_1.DatabaseConnection.open(dbPath);
+        const stale = this.db;
+        this.db = fresh;
+        this.queries = new queries_1.QueryBuilder(fresh.getDb());
+        this.wireLayers();
+        // Releasing the dead handle also frees the leaked db/-wal/-shm fds that were
+        // pinning the unlinked inode (#925).
+        try {
+            stale.close();
+        }
+        catch { /* the old inode is gone; closing just frees fds */ }
+        return true;
+    }
+    // ===========================================================================
+    // Lifecycle Methods
+    // ===========================================================================
+    /**
+     * Initialize a new CodeGraph project
+     *
+     * Creates the .CodeGraph directory, database, and configuration.
+     *
+     * @param projectRoot - Path to the project root directory
+     * @param options - Initialization options
+     * @returns A new CodeGraph instance
+     */
+    static async init(projectRoot, options = {}) {
+        await (0, extraction_1.initGrammars)();
+        const resolvedRoot = path.resolve(projectRoot);
+        // Check if already initialized
+        if ((0, directory_1.isInitialized)(resolvedRoot)) {
+            throw new Error(`CodeGraph already initialized in ${resolvedRoot}`);
+        }
+        // Create directory structure
+        (0, directory_1.createDirectory)(resolvedRoot);
+        // Initialize database
+        const dbPath = (0, db_1.getDatabasePath)(resolvedRoot);
+        const db = db_1.DatabaseConnection.initialize(dbPath);
+        const queries = new queries_1.QueryBuilder(db.getDb());
+        const instance = new CodeGraph(db, queries, resolvedRoot);
+        // Run initial indexing if requested
+        if (options.index) {
+            await instance.indexAll({ onProgress: options.onProgress });
+        }
+        return instance;
+    }
+    /**
+     * Initialize synchronously (without indexing)
+     */
+    static initSync(projectRoot) {
+        const resolvedRoot = path.resolve(projectRoot);
+        // Check if already initialized
+        if ((0, directory_1.isInitialized)(resolvedRoot)) {
+            throw new Error(`CodeGraph already initialized in ${resolvedRoot}`);
+        }
+        // Create directory structure
+        (0, directory_1.createDirectory)(resolvedRoot);
+        // Initialize database
+        const dbPath = (0, db_1.getDatabasePath)(resolvedRoot);
+        const db = db_1.DatabaseConnection.initialize(dbPath);
+        const queries = new queries_1.QueryBuilder(db.getDb());
+        return new CodeGraph(db, queries, resolvedRoot);
+    }
+    /**
+     * Open an existing CodeGraph project
+     *
+     * @param projectRoot - Path to the project root directory
+     * @param options - Open options
+     * @returns A CodeGraph instance
+     */
+    static async open(projectRoot, options = {}) {
+        await (0, extraction_1.initGrammars)();
+        const resolvedRoot = path.resolve(projectRoot);
+        // Check if initialized
+        if (!(0, directory_1.isInitialized)(resolvedRoot)) {
+            throw new Error(`CodeGraph not initialized in ${resolvedRoot}. Run init() first.`);
+        }
+        // Validate directory structure
+        const validation = (0, directory_1.validateDirectory)(resolvedRoot);
+        if (!validation.valid) {
+            throw new Error(`Invalid CodeGraph directory: ${validation.errors.join(', ')}`);
+        }
+        // Open database
+        const dbPath = (0, db_1.getDatabasePath)(resolvedRoot);
+        const db = db_1.DatabaseConnection.open(dbPath);
+        const queries = new queries_1.QueryBuilder(db.getDb());
+        const instance = new CodeGraph(db, queries, resolvedRoot);
+        // Sync if requested
+        if (options.sync) {
+            await instance.sync();
+        }
+        return instance;
+    }
+    /**
+     * Rebuild the project's database from scratch and return a fresh, empty
+     * instance — the "same result as a fresh init" semantics that `codegraph
+     * index` documents.
+     *
+     * Unlike `open()` followed by `clear()`, this DISCARDS the existing
+     * `.codegraph/codegraph.db` (and its `-wal`/`-shm` sidecars) before
+     * re-initializing, instead of opening the old database and DELETE-ing every
+     * row. On a large or pre-fix poisoned index — e.g. an old graph that scanned
+     * an ignored gitlink corpus (#1065) into ~1.6M nodes with a multi-GB WAL —
+     * the per-row `nodes_fts` delete-trigger churn blocks the main thread long
+     * enough to trip the #850 liveness watchdog before indexing even starts, so a
+     * full re-index could never recover the bad state (#1067). Discarding the
+     * files is O(1) regardless of size, reclaims the disk, and sidesteps opening
+     * (and running migrations against) the poisoned database entirely.
+     */
+    static async recreate(projectRoot) {
+        await (0, extraction_1.initGrammars)();
+        const resolvedRoot = path.resolve(projectRoot);
+        // Check if initialized — recreate REBUILDS an existing project; it is not a
+        // first-time `init`.
+        if (!(0, directory_1.isInitialized)(resolvedRoot)) {
+            throw new Error(`CodeGraph not initialized in ${resolvedRoot}. Run init() first.`);
+        }
+        const dbPath = (0, db_1.getDatabasePath)(resolvedRoot);
+        try {
+            (0, db_1.removeDatabaseFiles)(dbPath);
+        }
+        catch (err) {
+            // POSIX unlinks an open file fine; this fires mainly on Windows when a
+            // live daemon/MCP server still holds the database. Turn the raw EBUSY into
+            // an actionable instruction instead of a generic failure.
+            const reason = err instanceof Error ? err.message : String(err);
+            throw new Error(`Could not rebuild the index — the database file is in use (${reason}). ` +
+                `Stop any running CodeGraph MCP server/daemon for this project and retry, ` +
+                `or remove the ${(0, directory_2.getCodeGraphDir)(resolvedRoot)} directory and run "codegraph init".`);
+        }
+        // Re-create an empty, freshly-schema'd database at the same path.
+        const db = db_1.DatabaseConnection.initialize(dbPath);
+        const queries = new queries_1.QueryBuilder(db.getDb());
+        return new CodeGraph(db, queries, resolvedRoot);
+    }
+    /**
+     * Open synchronously (without sync)
+     */
+    static openSync(projectRoot) {
+        const resolvedRoot = path.resolve(projectRoot);
+        // Check if initialized
+        if (!(0, directory_1.isInitialized)(resolvedRoot)) {
+            throw new Error(`CodeGraph not initialized in ${resolvedRoot}. Run init() first.`);
+        }
+        // Validate directory structure
+        const validation = (0, directory_1.validateDirectory)(resolvedRoot);
+        if (!validation.valid) {
+            throw new Error(`Invalid CodeGraph directory: ${validation.errors.join(', ')}`);
+        }
+        // Open database
+        const dbPath = (0, db_1.getDatabasePath)(resolvedRoot);
+        const db = db_1.DatabaseConnection.open(dbPath);
+        const queries = new queries_1.QueryBuilder(db.getDb());
+        return new CodeGraph(db, queries, resolvedRoot);
+    }
+    /**
+     * Check if a directory has been initialized as a CodeGraph project
+     */
+    static isInitialized(projectRoot) {
+        return (0, directory_1.isInitialized)(path.resolve(projectRoot));
+    }
+    /**
+     * Close the CodeGraph instance and release resources
+     */
+    close() {
+        this.unwatch();
+        // Release file lock if held
+        this.fileLock.release();
+        this.db.close();
+    }
+    /**
+     * Get the project root directory
+     */
+    getProjectRoot() {
+        return this.projectRoot;
+    }
+    // ===========================================================================
+    // Indexing
+    // ===========================================================================
+    /**
+     * Index all files in the project
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    async indexAll(options = {}) {
+        return this.indexMutex.withLock(async () => {
+            try {
+                this.fileLock.acquire();
+            }
+            catch {
+                return { success: false, filesIndexed: 0, filesSkipped: 0, filesErrored: 0, nodesCreated: 0, edgesCreated: 0, errors: [{ message: 'Could not acquire file lock - another process may be indexing', severity: 'error' }], durationMs: 0 };
+            }
+            // Defer WAL auto-checkpointing for the whole bulk run (#1231): the
+            // default 1000-page interval re-writes hot pages into the main DB file
+            // over and over — ~95% of all disk I/O during a bulk index, and a
+            // 19+min → 45s difference on HDD-class storage. The valve bounds WAL
+            // growth by backfilling PASSIVEly on a worker thread (never blocking
+            // the writer or the #850 watchdog heartbeat); runMaintenance below does
+            // the final fold-up before the interval is restored in the finally.
+            // Kill switch: CODEGRAPH_NO_WAL_DEFER=1. Non-WAL journal modes (some
+            // network filesystems) have no WAL to defer — skip.
+            // Fast-init: on a COMPLETELY fresh DB, trade crash-durability for speed
+            // during the bulk build (journal in memory, no fsync). Safe because the
+            // DB is disposable until the index completes — index_state stays
+            // 'indexing' and a crashed init is re-run from scratch; existing DBs
+            // (re-index/sync) never take this path. Kill switch:
+            // CODEGRAPH_NO_FAST_INIT=1 (same pattern as CODEGRAPH_NO_WAL_DEFER).
+            const freshDb = this.queries.getNodeAndEdgeCount().nodes === 0;
+            const fastInit = process.env.CODEGRAPH_NO_FAST_INIT !== '1' && freshDb;
+            if (fastInit) {
+                try {
+                    this.db.getDb().pragma('journal_mode = MEMORY');
+                    this.db.getDb().pragma('synchronous = OFF');
+                }
+                catch { /* keep WAL */ }
+            }
+            const deferWal = !fastInit && process.env.CODEGRAPH_NO_WAL_DEFER !== '1' && this.db.getJournalMode() === 'wal';
+            let walValve = null;
+            let priorAutocheckpoint = 1000;
+            // Set when the fastInit+pool path below defers autocheckpointing, so the
+            // finally knows to restore the interval on that path too.
+            let restoreAutocheckpoint = false;
+            if (deferWal) {
+                priorAutocheckpoint = this.db.getWalAutocheckpoint();
+                this.db.setWalAutocheckpoint(0);
+                walValve = new wal_valve_1.WalCheckpointValve(this.db, undefined, undefined, options.verbose ? (m) => console.log(`[wal-valve] ${m}`) : undefined);
+                walValve.start();
+            }
+            try {
+                const before = this.queries.getNodeAndEdgeCount();
+                // Mark the index as in-flight BEFORE any writes: a run killed
+                // mid-index (OOM, SIGKILL, the #850 liveness watchdog) leaves this
+                // marker behind, so `codegraph status` can tell a truncated index
+                // from a completed one instead of silently serving partial results.
+                try {
+                    this.queries.setMetadata('index_state', 'indexing');
+                }
+                catch { /* metadata is advisory */ }
+                // Segment vocabulary starts empty and is repopulated by the node write
+                // path as every file (re-)indexes below — so a full index is also the
+                // orphan-cleanup pass for names deleted since the last one.
+                try {
+                    this.queries.clearNameSegmentVocab();
+                }
+                catch { /* vocab is advisory — never fail an index over it */ }
+                // Bulk FTS mode for the mass-insert phase: drop the per-row FTS sync
+                // triggers, rebuild nodes_fts once from the nodes table afterwards.
+                // Crash inside the window is healed on the next DatabaseConnection.open.
+                this.db.beginBulkNodeLoad();
+                let result;
+                try {
+                    result = await this.orchestrator.indexAll(options.onProgress, options.signal, options.verbose, walValve ? () => walValve.backpressure() : undefined, 
+                    // Store-writer offload is fresh-DB-only: with any pre-existing
+                    // data the store path must read (existing-file checks, cross-file
+                    // edge snapshots) and delete, which belongs on one thread.
+                    freshDb ? { dbPath: this.db.getPath(), fastInit } : null);
+                }
+                finally {
+                    const tFts = Date.now();
+                    this.db.endBulkNodeLoad();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[phase-timing] fts-rebuild: ${Date.now() - tFts}ms`);
+                }
+                // Fold the parse phase's WAL BEFORE the first post-parse reads
+                // (resolver re-init and resolution both read on the main thread):
+                // paging a bulk-write-sized WAL there is what blew the #850
+                // watchdog's 60s window in the #1231 repro. Off-thread + awaited,
+                // so the event loop keeps turning.
+                if (walValve)
+                    await walValve.foldNow();
+                // Re-detect frameworks now that the index is populated. The resolver
+                // is constructed with createResolver() before any files exist, so
+                // framework resolvers whose detect() consults the indexed file list
+                // (e.g. UIKit/SwiftUI scanning for imports, swift-objc-bridge looking
+                // for both Swift and ObjC files) all return false on that initial pass
+                // and silently drop themselves. Re-initializing here gives them a
+                // chance to see the actual project before resolution runs.
+                if (result.success && result.filesIndexed > 0) {
+                    const tReinit = Date.now();
+                    this.resolver.initialize();
+                    // Cross-file finalization (e.g. NestJS RouterModule prefixes). Runs
+                    // before resolution so updated names show up in subsequent reads.
+                    this.resolver.runPostExtract();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[phase-timing] resolver-reinit: ${Date.now() - tReinit}ms`);
+                }
+                // Resolve references to create call/import/extends edges
+                if (result.success && result.filesIndexed > 0) {
+                    // Get count without loading all refs into memory
+                    const unresolvedCount = this.queries.getUnresolvedReferencesCount();
+                    // Fast-init leaves the DB in memory-journal (rollback) mode, where
+                    // the parallel resolver pool's read connections would contend with
+                    // the main writer's exclusive commits. When the pool will actually
+                    // run (enough pending refs), restore WAL BEFORE resolution so
+                    // readers never block the writer; otherwise stay in the fast mode
+                    // until the finally — sequential resolution has no readers.
+                    if (fastInit && unresolvedCount >= (0, resolver_pool_1.minRefsForPool)()) {
+                        try {
+                            this.db.getDb().pragma('synchronous = NORMAL');
+                            this.db.getDb().pragma('journal_mode = WAL');
+                            // Defer auto-checkpointing for the resolution phase, same
+                            // rationale as the deferWal path above: at the default 1000-page
+                            // interval, the persist loop's edge inserts + ref deletes make
+                            // SQLite re-write hot B-tree pages into the main DB file inline
+                            // on the writer over and over (#1231's pathology — measured as
+                            // ~58% of the resolution phase on a 255k-ref repo). The valve
+                            // bounds WAL growth off-thread; runMaintenance does the final
+                            // fold and the finally restores the interval.
+                            priorAutocheckpoint = this.db.getWalAutocheckpoint();
+                            this.db.setWalAutocheckpoint(0);
+                            restoreAutocheckpoint = true;
+                            walValve = new wal_valve_1.WalCheckpointValve(this.db, undefined, undefined, options.verbose ? (m) => console.log(`[wal-valve] ${m}`) : undefined);
+                            walValve.start();
+                        }
+                        catch { /* keep current mode; resolution still works sequentially */ }
+                    }
+                    options.onProgress?.({
+                        phase: 'resolving',
+                        current: 0,
+                        total: unresolvedCount,
+                    });
+                    const tResolve = Date.now();
+                    await this.resolveReferencesBatched((current, total) => {
+                        options.onProgress?.({
+                            phase: 'resolving',
+                            current,
+                            total,
+                        });
+                    }, (done, totalPasses) => {
+                        options.onProgress?.({
+                            phase: 'linking',
+                            current: done,
+                            total: totalPasses,
+                        });
+                    });
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[phase-timing] resolution: ${Date.now() - tResolve}ms`);
+                    // Second pass: chained calls whose method lives on a supertype the
+                    // receiver conforms to (protocol-extension / inherited / default-
+                    // interface). Needs the implements/extends edges the main pass just
+                    // built, so it runs after resolution (#750).
+                    const tChained = Date.now();
+                    await this.resolver.resolveChainedCallsViaConformance();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[synth-timing] chainedConformance: ${Date.now() - tChained}ms`);
+                    // Same lifecycle for `this.<member>` callback registrations whose
+                    // member is inherited from a supertype (#808).
+                    const tDeferred = Date.now();
+                    await this.resolver.resolveDeferredThisMemberRefs();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[synth-timing] deferredThisMember: ${Date.now() - tDeferred}ms`);
+                }
+                // Refresh planner stats + checkpoint the WAL after bulk writes.
+                // Off-thread (worker connection): on a multi-GB index this is minutes
+                // of IO, and inline it starved the #850 watchdog AFTER a fully
+                // successful index. Never load-bearing for correctness.
+                if (result.success && result.filesIndexed > 0) {
+                    const tMaint = Date.now();
+                    // Quiesce the valve first so its in-flight checkpoint and the
+                    // maintenance checkpoint don't contend for the checkpointer lock
+                    // (the loser would silently no-op and leave the WAL unfolded).
+                    if (walValve) {
+                        walValve.stop();
+                        await walValve.drain();
+                    }
+                    await this.db.runMaintenance();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[phase-timing] maintenance: ${Date.now() - tMaint}ms`);
+                }
+                // The orchestrator only sees extraction-phase counts; resolution and
+                // synthesizer edges (often >50% of the graph on JVM repos) come later.
+                // Recompute against the DB so the CLI summary reports the true totals.
+                if (result.success && result.filesIndexed > 0) {
+                    const tCount = Date.now();
+                    const after = this.queries.getNodeAndEdgeCount();
+                    if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                        console.error(`[phase-timing] count-recompute: ${Date.now() - tCount}ms`);
+                    result.nodesCreated = after.nodes - before.nodes;
+                    result.edgesCreated = after.edges - before.edges;
+                }
+                // Stamp the index with the engine that built it, so `codegraph status`
+                // and `codegraph upgrade` can recommend a re-index when the running
+                // engine produces richer extraction than the one on disk. Only on a
+                // real full index — a sync touches a subset, so it must NOT advance the
+                // extraction stamp (the bulk would still be stale). See extraction-version.ts.
+                if (result.success && result.filesIndexed > 0) {
+                    try {
+                        this.queries.setMetadata('indexed_with_version', version_1.CodeGraphPackageVersion);
+                        this.queries.setMetadata('indexed_with_extraction_version', String(extraction_version_1.EXTRACTION_VERSION));
+                    }
+                    catch { /* metadata is advisory — never fail an index over it */ }
+                }
+                // Reconcile the scan's ground truth against what the pipeline
+                // accounted for. A shortfall means files were silently dropped
+                // (observed in the wild: a run under heavy load came up 37 files
+                // short with no error) — record it and tell the user, don't let the
+                // index pass as complete.
+                try {
+                    if (!result.success) {
+                        this.queries.setMetadata('index_state', 'failed');
+                    }
+                    else {
+                        const accounted = result.filesIndexed + result.filesSkipped + result.filesErrored;
+                        const discovered = result.filesDiscovered;
+                        const shortfall = discovered !== undefined ? discovered - accounted : 0;
+                        if (discovered !== undefined && shortfall > 0) {
+                            this.queries.setMetadata('index_state', 'partial');
+                            this.queries.setMetadata('index_files_discovered', String(discovered));
+                            this.queries.setMetadata('index_files_accounted', String(accounted));
+                            result.errors.push({
+                                message: `Index is missing ${shortfall} of ${discovered} discovered files (indexed ${result.filesIndexed}, skipped ${result.filesSkipped}, errored ${result.filesErrored}). The index is PARTIAL — re-run \`codegraph index\`.`,
+                                severity: 'warning',
+                                code: 'index_partial',
+                            });
+                        }
+                        else {
+                            this.queries.setMetadata('index_state', 'complete');
+                            if (discovered !== undefined) {
+                                this.queries.setMetadata('index_files_discovered', String(discovered));
+                                this.queries.setMetadata('index_files_accounted', String(accounted));
+                            }
+                        }
+                    }
+                }
+                catch { /* metadata is advisory — never fail an index over it */ }
+                return result;
+            }
+            finally {
+                // Restore the auto-checkpoint interval AFTER the fold-up above so the
+                // next ordinary write doesn't inherit a giant inline checkpoint. On
+                // the error path the WAL may still be large; correctness is unchanged
+                // (SQLite replays the WAL on the next open) and the follow-up write
+                // that folds it is the known cost of a failed run.
+                if (walValve) {
+                    walValve.stop();
+                    await walValve.drain();
+                }
+                if (deferWal || restoreAutocheckpoint) {
+                    try {
+                        this.db.setWalAutocheckpoint(priorAutocheckpoint);
+                    }
+                    catch { /* connection may be closing */ }
+                }
+                if (fastInit) {
+                    // Back to the durable defaults; journal_mode=WAL folds the MEMORY
+                    // journal state into a normal WAL-mode database file.
+                    try {
+                        this.db.getDb().pragma('synchronous = NORMAL');
+                        this.db.getDb().pragma('journal_mode = WAL');
+                    }
+                    catch { /* connection may be closing */ }
+                }
+                this.fileLock.release();
+            }
+        });
+    }
+    /**
+     * Index specific files
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    async indexFiles(filePaths) {
+        return this.indexMutex.withLock(async () => {
+            try {
+                this.fileLock.acquire();
+            }
+            catch {
+                return { success: false, filesIndexed: 0, filesSkipped: 0, filesErrored: 0, nodesCreated: 0, edgesCreated: 0, errors: [{ message: 'Could not acquire file lock - another process may be indexing', severity: 'error' }], durationMs: 0 };
+            }
+            try {
+                return this.orchestrator.indexFiles(filePaths);
+            }
+            finally {
+                this.fileLock.release();
+            }
+        });
+    }
+    /**
+     * Sync with current file state (incremental update)
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    async sync(options = {}) {
+        return this.indexMutex.withLock(async () => {
+            try {
+                this.fileLock.acquire();
+            }
+            catch {
+                return { filesChecked: 0, filesAdded: 0, filesModified: 0, filesRemoved: 0, nodesUpdated: 0, durationMs: 0 };
+            }
+            // Defer WAL auto-checkpointing for the whole incremental run, exactly
+            // as indexAll does for the bulk path (#1231): sync's store loop and its
+            // resolution passes churn the same FTS + secondary-index hot pages, and
+            // at the default 1000-page cadence the inline checkpoints re-write them
+            // over and over — on HDD-class storage a 7-file sync took 2 minutes at
+            // 0-2% CPU (#1248). The cost scales with the EXISTING database size,
+            // not the change size, so small syncs on big indexes hurt most. The
+            // valve bounds WAL growth off-thread; runMaintenance at the end does
+            // the final fold-up before the interval is restored in the finally.
+            // Same kill switch as indexAll: CODEGRAPH_NO_WAL_DEFER=1. Idle valve
+            // cost is one timer, so watcher-frequency syncs stay cheap.
+            const deferWal = process.env.CODEGRAPH_NO_WAL_DEFER !== '1' && this.db.getJournalMode() === 'wal';
+            let walValve = null;
+            let priorAutocheckpoint = 1000;
+            if (deferWal) {
+                priorAutocheckpoint = this.db.getWalAutocheckpoint();
+                this.db.setWalAutocheckpoint(0);
+                walValve = new wal_valve_1.WalCheckpointValve(this.db, undefined, undefined, options.verbose ? (m) => console.log(`[wal-valve] ${m}`) : undefined);
+                walValve.start();
+            }
+            try {
+                // Captured BEFORE the sync runs: the sync's own incremental writes
+                // populate vocab rows for the files it touches, so an end-of-sync
+                // emptiness check would see "non-empty" and skip the backfill forever,
+                // leaving every unchanged file's names unsegmented.
+                const vocabWasEmpty = (() => {
+                    try {
+                        return this.queries.isNameSegmentVocabEmpty();
+                    }
+                    catch {
+                        return false;
+                    }
+                })();
+                const result = await this.orchestrator.sync(options.onProgress);
+                // Fold the store phase's WAL BEFORE the post-store reads below
+                // (resolution reads on the main thread) — same rationale as
+                // indexAll's fold between store and resolution.
+                if (walValve)
+                    await walValve.foldNow();
+                // Cross-file finalization (e.g. NestJS RouterModule prefixes). Run on
+                // every sync that touched files so edits to `app.module.ts` propagate
+                // to controllers in unchanged files. The pass is idempotent and cheap
+                // (regex over *.module.ts only).
+                if (result.filesAdded > 0 || result.filesModified > 0) {
+                    this.resolver.runPostExtract();
+                }
+                else if (result.filesRemoved > 0) {
+                    // A pure-removal sync still resolves refs below — the deletion path
+                    // resurrects the removed file's incoming edges as pending refs
+                    // (#1240 removal case) and the orphan sweep consumes them. In a
+                    // long-lived process (daemon) the resolver's name caches were
+                    // warmed against the pre-removal graph; drop them so resolution
+                    // sees the post-removal state. (runPostExtract above clears caches
+                    // itself, so the changed-files branch is already covered.)
+                    this.resolver.clearCaches();
+                }
+                // Resolve references if files were updated
+                const filesChanged = result.filesAdded > 0 || result.filesModified > 0;
+                if (filesChanged) {
+                    if (result.changedFilePaths) {
+                        // Scope resolution to changed files (git fast path — bounded set)
+                        const tRefLoad = Date.now();
+                        const unresolvedRefs = this.queries.getUnresolvedReferencesByFiles(result.changedFilePaths);
+                        if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                            console.error(`[phase-timing] sync-ref-load: ${Date.now() - tRefLoad}ms (${unresolvedRefs.length} refs)`);
+                        options.onProgress?.({
+                            phase: 'resolving',
+                            current: 0,
+                            total: unresolvedRefs.length,
+                        });
+                        this.resolver.resolveAndPersist(unresolvedRefs, (current, total) => {
+                            options.onProgress?.({
+                                phase: 'resolving',
+                                current,
+                                total,
+                            });
+                        });
+                        // Retry previously-failed refs the changed files may now satisfy
+                        // (#1240). Scoped resolution above only re-resolves refs FROM the
+                        // changed files — but when a changed file gains an export/symbol,
+                        // refs in UNCHANGED files that failed against the old graph can
+                        // now resolve, and nothing else ever revisits them (their rows
+                        // were parked as status='failed' by an earlier completed pass).
+                        // Look them up by the symbol names the changed files now carry
+                        // and re-resolve just that set. On a sync where no failed ref
+                        // matches, this is one indexed lookup.
+                        const tRetry = Date.now();
+                        const retryable = this.queries.getRetryableFailedReferences(this.queries.getNodeNamesByFiles(result.changedFilePaths));
+                        if (retryable.length > 0) {
+                            options.onProgress?.({
+                                phase: 'resolving',
+                                current: 0,
+                                total: retryable.length,
+                            });
+                            await this.resolver.resolveAndPersistListYielding(retryable);
+                            options.onProgress?.({
+                                phase: 'resolving',
+                                current: retryable.length,
+                                total: retryable.length,
+                            });
+                        }
+                        if (process.env.CODEGRAPH_SYNTH_TIMINGS)
+                            console.error(`[phase-timing] sync-failed-ref-retry: ${Date.now() - tRetry}ms (${retryable.length} refs)`);
+                    }
+                    else {
+                        // No git info — use batched resolution to avoid OOM
+                        const unresolvedCount = this.queries.getUnresolvedReferencesCount();
+                        options.onProgress?.({
+                            phase: 'resolving',
+                            current: 0,
+                            total: unresolvedCount,
+                        });
+                        await this.resolveReferencesBatched((current, total) => {
+                            options.onProgress?.({
+                                phase: 'resolving',
+                                current,
+                                total,
+                            });
+                        }, (done, totalPasses) => {
+                            options.onProgress?.({
+                                phase: 'linking',
+                                current: done,
+                                total: totalPasses,
+                            });
+                        });
+                    }
+                }
+                // Orphan sweep (#1187). A resolution pass that dies mid-run — the #850
+                // daemon liveness watchdog's SIGKILL (#1122), Ctrl-C, a crash — leaves
+                // the refs it never reached in unresolved_refs, and the git-scoped fast
+                // path above never revisits them (it reads only the changed files'
+                // rows). Those files' call edges were then missing PERMANENTLY, with
+                // nothing to see except a too-small blast radius, until a full
+                // re-index. A completed pass takes every row it processed out of the
+                // PENDING set (resolved rows are deleted, unresolvable ones parked as
+                // status='failed' for the #1240 retry above), so any pending row now
+                // is such an orphan — or a row from an older engine's scoped pass.
+                // Grind them down with the batched resolver; this also makes a bare
+                // `codegraph sync` the recovery command for a wedged index. On a
+                // healthy index this is one COUNT query.
+                const orphanCount = this.queries.getUnresolvedReferencesCount();
+                if (orphanCount > 0) {
+                    options.onProgress?.({
+                        phase: 'resolving',
+                        current: 0,
+                        total: orphanCount,
+                    });
+                    await this.resolveReferencesBatched((current, total) => {
+                        options.onProgress?.({
+                            phase: 'resolving',
+                            current,
+                            total,
+                        });
+                    }, (done, totalPasses) => {
+                        options.onProgress?.({
+                            phase: 'linking',
+                            current: done,
+                            total: totalPasses,
+                        });
+                    });
+                }
+                if (filesChanged || orphanCount > 0) {
+                    // Second pass: chained calls whose method lives on a supertype the
+                    // receiver conforms to (protocol-extension / inherited). Needs the
+                    // implements/extends edges built above (#750).
+                    await this.resolver.resolveChainedCallsViaConformance();
+                    // Same lifecycle for `this.<member>` callback registrations whose
+                    // member is inherited from a supertype (#808).
+                    await this.resolver.resolveDeferredThisMemberRefs();
+                }
+                // Refresh planner stats + checkpoint the WAL after bulk writes.
+                // Off-thread — see indexAll's call site.
+                if (filesChanged || result.filesRemoved > 0 || orphanCount > 0) {
+                    await this.db.runMaintenance();
+                }
+                // Heal the segment vocabulary on indexes built before the table
+                // existed (upgrade path): incremental writes above only cover changed
+                // files, so a vocab that was empty when this sync STARTED means the
+                // bulk was never segmented — backfill it (INSERT OR IGNORE, so the
+                // rows the sync just wrote are fine). Batched + yielding — sync can
+                // run on the daemon's liveness-watchdog thread (#850/#1091).
+                try {
+                    if (vocabWasEmpty && this.queries.getNodeAndEdgeCount().nodes > 0) {
+                        await this.rebuildNameSegmentVocab();
+                    }
+                }
+                catch { /* vocab is advisory — never fail a sync over it */ }
+                return result;
+            }
+            finally {
+                // Mirror indexAll's teardown: stop the valve, then restore the
+                // auto-checkpoint interval (runMaintenance above already folded the
+                // WAL on the success path; on the error path SQLite replays it on
+                // the next open).
+                if (walValve) {
+                    walValve.stop();
+                    await walValve.drain();
+                }
+                if (deferWal) {
+                    try {
+                        this.db.setWalAutocheckpoint(priorAutocheckpoint);
+                    }
+                    catch { /* connection may be closing */ }
+                }
+                this.fileLock.release();
+            }
+        });
+    }
+    /**
+     * Check if an indexing operation is currently in progress
+     */
+    isIndexing() {
+        return this.indexMutex.isLocked();
+    }
+    // ===========================================================================
+    // File Watching
+    // ===========================================================================
+    /**
+     * Start watching for file changes and auto-syncing.
+     *
+     * Uses native OS file events (FSEvents on macOS, inotify on Linux 19+,
+     * ReadDirectoryChangesW on Windows) with debouncing to avoid thrashing.
+     *
+     * @param options - Watch options (debounce delay, callbacks)
+     * @returns true if watching started successfully
+     */
+    watch(options = {}) {
+        if (this.watcher?.isActive())
+            return true;
+        this.watcher = new sync_1.FileWatcher(this.projectRoot, async () => {
+            const result = await this.sync();
+            // sync() returns this exact zero-shape iff it failed to acquire the
+            // file lock (a real empty sync always has filesChecked > 0 because
+            // scanDirectory ran). Surface that to the watcher as a typed error
+            // so it keeps pendingFiles + reschedules instead of clearing them
+            // (#449).
+            if (result.filesChecked === 0 && result.durationMs === 0) {
+                throw new sync_1.LockUnavailableError();
+            }
+            const filesChanged = result.filesAdded + result.filesModified + result.filesRemoved;
+            return { filesChanged, durationMs: result.durationMs };
+        }, options);
+        return this.watcher.start();
+    }
+    /**
+     * Stop watching for file changes.
+     */
+    unwatch() {
+        if (this.watcher) {
+            this.watcher.stop();
+            this.watcher = null;
+        }
+    }
+    /**
+     * Check if the file watcher is active.
+     */
+    isWatching() {
+        return this.watcher?.isActive() ?? false;
+    }
+    /**
+     * True once live watching has permanently degraded (OS watch-resource
+     * exhaustion, or a write lock held past the retry budget) and auto-sync is
+     * disabled until the next {@link watch} call. Distinct from `!isWatching()`:
+     * a stopped/never-started watcher is inactive but NOT degraded. MCP tools use
+     * this to surface a whole-index "results may be stale" notice, since
+     * `getPendingFiles()` goes empty once watching stops (#876).
+     */
+    isWatcherDegraded() {
+        return this.watcher?.isDegraded() ?? false;
+    }
+    /** The reason live watching degraded, or null if it is healthy (#876). */
+    getWatcherDegradedReason() {
+        return this.watcher?.getDegradedReason() ?? null;
+    }
+    /**
+     * Files seen by the file watcher since the last successful sync —
+     * the per-file "stale" signal MCP tools attach to responses so an agent
+     * can fall back to {@link Read} for just the affected file without
+     * waiting for a debounced sync to complete (issue #403).
+     *
+     * Returns an empty list when the watcher isn't active, or no events have
+     * arrived. Each entry includes `firstSeenMs` and `lastSeenMs` (wall-clock
+     * `Date.now()` values) so callers can render "edited Nms ago", plus an
+     * `indexing` flag indicating whether the in-flight sync (if any) will
+     * absorb that file.
+     */
+    getPendingFiles() {
+        return this.watcher?.getPendingFiles() ?? [];
+    }
+    /**
+     * Resolves once the file watcher has installed its watch set. Useful for
+     * tests that need a deterministic boundary before asserting on
+     * `getPendingFiles()`. Resolves immediately when no watcher is active.
+     */
+    waitUntilWatcherReady(timeoutMs) {
+        return this.watcher ? this.watcher.waitUntilReady(timeoutMs) : Promise.resolve();
+    }
+    /**
+     * Get files that have changed since last index
+     */
+    getChangedFiles() {
+        return this.orchestrator.getChangedFiles();
+    }
+    /**
+     * Most recent index timestamp (ms since epoch) across all tracked files, or
+     * null when nothing is indexed yet. Lets library consumers check index
+     * freshness without shelling out to `codegraph status --json`. (#329)
+     */
+    getLastIndexedAt() {
+        return this.queries.getLastIndexedAt();
+    }
+    /**
+     * Completeness of the last full index run. `'complete'` is the only good
+     * state. `'indexing'` after the fact means a run was killed mid-index (OOM,
+     * SIGKILL, liveness watchdog) and the on-disk index is truncated;
+     * `'partial'` means the run finished but silently dropped files
+     * (discovered > indexed+skipped+errored); `'failed'` means it reported
+     * failure. `null` = index predates this marker. Surfaced by
+     * `codegraph status`.
+     */
+    getIndexState() {
+        const raw = this.queries.getMetadata('index_state');
+        return raw === 'indexing' || raw === 'complete' || raw === 'partial' || raw === 'failed'
+            ? raw
+            : null;
+    }
+    /**
+     * Which engine built the current index: the package version + extraction
+     * version stamped at the last full `indexAll`. Either field is null for an
+     * index built before stamping existed (treated as stale). See
+     * `extraction-version.ts` and `isIndexStale()`.
+     */
+    getIndexBuildInfo() {
+        const version = this.queries.getMetadata('indexed_with_version');
+        const ev = this.queries.getMetadata('indexed_with_extraction_version');
+        const parsed = ev != null ? parseInt(ev, 10) : NaN;
+        return { version, extractionVersion: Number.isFinite(parsed) ? parsed : null };
+    }
+    /**
+     * True when the on-disk index was built by an engine whose extraction is
+     * older than the one now running — i.e. a re-index would add data a migration
+     * can't backfill. False when there's no index yet (nothing to refresh) or the
+     * stamp is current. This is the signal behind `codegraph status`'s re-index
+     * hint and `codegraph upgrade`'s reminder.
+     */
+    isIndexStale() {
+        if (this.queries.getLastIndexedAt() == null)
+            return false;
+        const { extractionVersion } = this.getIndexBuildInfo();
+        return extractionVersion == null || extractionVersion < extraction_version_1.EXTRACTION_VERSION;
+    }
+    /**
+     * Extract nodes and edges from source code (without storing)
+     */
+    extractFromSource(filePath, source) {
+        return (0, extraction_1.extractFromSource)(filePath, source);
+    }
+    // ===========================================================================
+    // Reference Resolution
+    // ===========================================================================
+    /**
+     * Resolve unresolved references and create edges
+     *
+     * This method takes unresolved references from extraction and attempts
+     * to resolve them using multiple strategies:
+     * - Framework-specific patterns (React, Express, Laravel)
+     * - Import-based resolution
+     * - Name-based symbol matching
+     */
+    resolveReferences(onProgress) {
+        // Get all unresolved references from the database
+        const unresolvedRefs = this.queries.getUnresolvedReferences();
+        return this.resolver.resolveAndPersist(unresolvedRefs, onProgress);
+    }
+    /**
+     * Resolve references in batches to keep memory bounded on large codebases.
+     * Processes chunks of unresolved refs, persisting results after each batch.
+     */
+    async resolveReferencesBatched(onProgress, onSynthesisProgress) {
+        return this.resolver.resolveAndPersistBatched(onProgress, undefined, onSynthesisProgress, {
+            dbPath: this.db.getPath(),
+            // Bulk-edge-load hooks: on big runs the resolver drops the non-unique
+            // edge indexes for the batch loop and recreates them before synthesis
+            // (which reads kind-keyed). Concurrent readers (a daemon serving this
+            // project mid-index) stay CORRECT during the window — target/kind reads
+            // just degrade to scans until the recreate.
+            bulkEdgeLoad: {
+                begin: () => this.db.beginBulkEdgeLoad(),
+                end: () => this.db.endBulkEdgeLoad(),
+            },
+        });
+    }
+    /**
+     * References extracted but never attempted by a resolution pass. Zero on a
+     * healthy index — a completed pass consumes every pending row (resolving it
+     * or parking it as failed, #1240). Non-zero at rest means a pass was
+     * interrupted mid-run (killed indexer, crash — #1187), so some files' call
+     * edges are missing; the next `sync` sweeps them.
+     */
+    getPendingReferenceCount() {
+        return this.queries.getUnresolvedReferencesCount();
+    }
+    /**
+     * Get detected frameworks in the project
+     */
+    getDetectedFrameworks() {
+        return this.resolver.getDetectedFrameworks();
+    }
+    /**
+     * Re-initialize the resolver (useful after adding new files)
+     */
+    reinitializeResolver() {
+        this.resolver.initialize();
+    }
+    // ===========================================================================
+    // Graph Statistics
+    // ===========================================================================
+    /**
+     * Get statistics about the knowledge graph
+     */
+    getStats() {
+        const stats = this.queries.getStats();
+        stats.dbSizeBytes = this.db.getSize();
+        return stats;
+    }
+    /**
+     * Active SQLite backend for this project's connection (`node-sqlite` — Node's
+     * built-in real-SQLite module). Surfaced via `codegraph status` and the
+     * `codegraph_status` MCP tool alongside the effective journal mode.
+     */
+    getBackend() {
+        return this.db.getBackend();
+    }
+    /**
+     * The journal mode actually in effect ('wal', 'delete', …). 'wal' means
+     * readers never block on a concurrent writer; anything else means they can,
+     * which is the precondition for the "database is locked" failures in issue
+     * #238. Surfaced via `codegraph status` and the `codegraph_status` MCP tool.
+     */
+    getJournalMode() {
+        return this.db.getJournalMode();
+    }
+    // ===========================================================================
+    // Node Operations
+    // ===========================================================================
+    /**
+     * Get a node by ID
+     */
+    getNode(id) {
+        return this.queries.getNodeById(id);
+    }
+    /**
+     * Get all nodes in a file
+     */
+    getNodesInFile(filePath) {
+        return this.queries.getNodesByFile(filePath);
+    }
+    /**
+     * Get all nodes of a specific kind
+     */
+    getNodesByKind(kind) {
+        return this.queries.getNodesByKind(kind);
+    }
+    /**
+     * Get ALL nodes with an exact name (direct index lookup, not FTS-ranked/capped).
+     * Used to enumerate every overload of a heavily-overloaded name so the specific
+     * definition the caller wants is never dropped below a search cut.
+     */
+    getNodesByName(name) {
+        return this.queries.getNodesByName(name);
+    }
+    /** Nodes whose name starts with `prefix` (index range scan, capped). */
+    getNodesByNamePrefix(prefix, limit = 20) {
+        return this.queries.getNodesByNamePrefix(prefix, limit);
+    }
+    /**
+     * Nodes whose name CONTAINS `substring` (LIKE scan, ASCII-case-insensitive,
+     * shortest-first). The camel-infix lookup FTS can't do — `profileInfo`
+     * inside `getProfileInfoV2` is one FTS token (#1196).
+     */
+    getNodesByNameSubstring(substring, options = {}) {
+        return this.queries
+            .findNodesByNameSubstring(substring, options)
+            .map((r) => r.node);
+    }
+    /**
+     * Search nodes by text
+     */
+    searchNodes(query, options) {
+        return this.queries.searchNodes(query, options);
+    }
+    /**
+     * Graph-derived prompt matching for the front-load hook's MEDIUM tier:
+     * which indexed symbols do these prose words name? "state machine des
+     * commandes" → `OrderStateMachine`, in any human language whose technical
+     * nouns are Latin script — no keyword list involved.
+     *
+     * Precision comes from the repo's own naming statistics, not vocabulary:
+     * - CO-OCCURRENCE: ≥2 words that are segments of the SAME name ("state" +
+     *   "machine" → OrderStateMachine) is strong evidence and always qualifies.
+     * - RARITY: a single matched word qualifies only when its segment is
+     *   discriminative here (≤ {@link SEGMENT_RARITY_CEILING} distinct names) —
+     *   "checkout" in a shop backend yes, "state" in a react app no.
+     * Every candidate is re-verified against `nodes` before being returned
+     * (vocab rows are proposals; deletions leave orphans by design), so a
+     * returned symbol is guaranteed to exist right now.
+     */
+    getSegmentMatches(words, limit = 6) {
+        if (words.length === 0)
+            return [];
+        // Variant → original word (plural folding), for coverage accounting.
+        const variantToWord = new Map();
+        for (const word of words) {
+            for (const variant of (0, identifier_segments_1.segmentLookupVariants)(word)) {
+                if (!variantToWord.has(variant))
+                    variantToWord.set(variant, word);
+            }
+        }
+        const variants = [...variantToWord.keys()];
+        // Tier A: co-occurrence. The SQL folds variants back to their original
+        // word (#1146), so minWords=2 means two distinct PROMPT WORDS — a name
+        // matching both `service` and `services` can't tie with (or crowd past
+        // the LIMIT) a genuine two-word match. The JS re-check below recomputes
+        // the fold from live segments as the honesty layer.
+        const variantPairs = [...variantToWord.entries()].map(([segment, word]) => ({ segment, word }));
+        const candidates = [];
+        for (const hit of this.queries.getSegmentCoOccurrence(variantPairs, 2, 24)) {
+            const matched = this.wordsMatchingName(hit.name, variantToWord);
+            if (matched.size >= 2)
+                candidates.push({ name: hit.name, matchedWords: matched });
+        }
+        // Tier B: single rare word. Only when co-occurrence found nothing — a
+        // co-occurring name is categorically stronger evidence — and under
+        // stricter rules, because one word is thin: the word must be ≥5 chars
+        // (measured FPs: "this", "typo"); the segment must appear in AT LEAST TWO
+        // names (a concept the codebase is about clusters across names —
+        // CheckoutService/CheckoutController — while a prose coincidence is a
+        // singleton: measured FP "deploy to PRODUCTION" → the one name
+        // matchesNonProductionDir); and the candidate name must have ≥2 segments
+        // (a bare common verb matching a bare function name — "write" → `write` —
+        // is prose coincidence, not the user naming a symbol).
+        if (candidates.length === 0) {
+            const singleWordVariants = variants.filter((v) => variantToWord.get(v).length >= 5);
+            const counts = this.queries.getSegmentNameCounts(singleWordVariants);
+            const rare = [...counts.entries()]
+                .filter(([, n]) => n >= 2 && n <= CodeGraph.SEGMENT_RARITY_CEILING)
+                .sort((a, b) => a[1] - b[1])
+                .slice(0, 2);
+            for (const [variant] of rare) {
+                const word = variantToWord.get(variant);
+                for (const name of this.queries.getNamesForSegment(variant, 12)) {
+                    if ((0, identifier_segments_1.splitIdentifierSegments)(name).length < 2)
+                        continue;
+                    candidates.push({ name, matchedWords: new Set([word]) });
+                }
+            }
+        }
+        // Verify against nodes (the honesty gate) and pick a representative
+        // definition per name. A name whose only nodes are file/import kind has
+        // no real definition to point at — surfacing the import statement instead
+        // reads as a matched symbol but isn't one (#1144) — so it's skipped, the
+        // same way an orphaned vocab row is. (Import names no longer enter the
+        // vocab at write time, but rows written before that exclusion persist
+        // until the next full index.)
+        const out = [];
+        const seen = new Set();
+        candidates.sort((a, b) => b.matchedWords.size - a.matchedWords.size || a.name.length - b.name.length);
+        for (const candidate of candidates) {
+            if (out.length >= limit)
+                break;
+            if (seen.has(candidate.name))
+                continue;
+            seen.add(candidate.name);
+            const nodes = this.queries.getNodesByName(candidate.name);
+            if (nodes.length === 0)
+                continue; // orphaned vocab row — name no longer exists
+            const rep = nodes.find((n) => n.kind !== 'file' && n.kind !== 'import');
+            if (!rep)
+                continue; // no real definition — don't surface an import/file as one
+            out.push({
+                name: candidate.name,
+                kind: rep.kind,
+                filePath: rep.filePath,
+                startLine: rep.startLine ?? 0,
+                matchedWords: [...candidate.matchedWords].sort(),
+            });
+        }
+        return out;
+    }
+    /** A single word ("state") can match hundreds of names in a big repo — that
+     *  is noise, not signal. Ceiling for the single-word tier; co-occurrence is
+     *  exempt because two words on one name is already discriminative. */
+    static SEGMENT_RARITY_CEILING = 25;
+    /** Which of the prompt's original words match `name`'s segments (via
+     *  variants). Segments are recomputed in JS — a name-keyed vocab lookup
+     *  would scan the (segment, name) primary key. */
+    wordsMatchingName(name, variantToWord) {
+        const segments = new Set((0, identifier_segments_1.splitIdentifierSegments)(name));
+        const matched = new Set();
+        for (const [variant, word] of variantToWord) {
+            if (segments.has(variant))
+                matched.add(word);
+        }
+        return matched;
+    }
+    /**
+     * One-shot upgrade heal for callers that open the graph WITHOUT syncing —
+     * concretely the prompt hook, whose MEDIUM tier reads the segment
+     * vocabulary: a database migrated from before the vocab table existed
+     * starts with it empty, and the only other backfill lives inside `sync()`,
+     * which such callers never run (#1142). Returns true when the vocab is
+     * usable (already populated — the overwhelmingly common one-SELECT case —
+     * or healed here); false when it isn't (empty graph, or another process
+     * holds the index lock — that process's own sync heals it).
+     */
+    async healSegmentVocabIfEmpty() {
+        const empty = (() => {
+            try {
+                return this.queries.isNameSegmentVocabEmpty();
+            }
+            catch {
+                return false;
+            }
+        })();
+        if (!empty)
+            return true;
+        if (this.queries.getNodeAndEdgeCount().nodes === 0)
+            return false;
+        return this.indexMutex.withLock(async () => {
+            try {
+                this.fileLock.acquire();
+            }
+            catch {
+                return false; // an index/sync is running — it backfills the vocab itself
+            }
+            try {
+                if (!this.queries.isNameSegmentVocabEmpty())
+                    return true; // raced: healed meanwhile
+                await this.rebuildNameSegmentVocab();
+                return true;
+            }
+            finally {
+                this.fileLock.release();
+            }
+        });
+    }
+    /**
+     * Rebuild the segment vocabulary from the current graph, batched and
+     * yielding — the upgrade-heal path for indexes built before the vocab table
+     * existed. Runs inside the index mutex/lock (sync and
+     * healSegmentVocabIfEmpty hold them).
+     */
+    async rebuildNameSegmentVocab() {
+        const maybeYield = (0, cooperative_yield_1.createYielder)();
+        const BATCH = 2000;
+        for (let offset = 0;; offset += BATCH) {
+            const names = this.queries.getDistinctNodeNames(BATCH, offset);
+            if (names.length === 0)
+                break;
+            this.queries.insertNameSegmentsBatch(names);
+            await maybeYield();
+        }
+    }
+    /**
+     * Normalized project-name tokens (go.mod / package.json / repo dir) used to
+     * down-weight the non-discriminative project name in search ranking (#720).
+     * Exposed so explore can exclude it from the PascalCase type-disambiguation
+     * bias, which would otherwise pull overloaded tokens toward whichever stack
+     * embeds the project name.
+     */
+    getProjectNameTokens() {
+        return this.queries.getProjectNameTokens();
+    }
+    /**
+     * Find the project's "primary route file" — the file with the densest
+     * concentration of framework-emitted `route` nodes (≥3 routes, ≥30%
+     * of all non-test routes). Used to inline the routing config in
+     * `codegraph_explore` responses on small realworld template repos
+     * (rails-realworld, laravel-realworld, drupal-admintoolbar, …) where
+     * Glob+Read of `routes.rb`/`urls.py`/etc. otherwise beats codegraph.
+     */
+    getTopRouteFile() {
+        return this.queries.getTopRouteFile();
+    }
+    /**
+     * Build a URL → handler routing manifest from the index. Each entry
+     * pairs a route node (URL + method) with its handler function/method
+     * via the `references` edge that framework resolvers emit. Returns
+     * null when fewer than 3 valid (non-test) routes exist.
+     */
+    getRoutingManifest(limit) {
+        return this.queries.getRoutingManifest(limit);
+    }
+    // ===========================================================================
+    // Edge Operations
+    // ===========================================================================
+    /**
+     * Get outgoing edges from a node
+     */
+    getOutgoingEdges(nodeId) {
+        return this.queries.getOutgoingEdges(nodeId);
+    }
+    /**
+     * Get incoming edges to a node
+     */
+    getIncomingEdges(nodeId) {
+        return this.queries.getIncomingEdges(nodeId);
+    }
+    // ===========================================================================
+    // File Operations
+    // ===========================================================================
+    /**
+     * Get a file record by path
+     */
+    getFile(filePath) {
+        return this.queries.getFileByPath(filePath);
+    }
+    /**
+     * Get all tracked files
+     */
+    getFiles() {
+        return this.queries.getAllFiles();
+    }
+    // ===========================================================================
+    // Graph Query Methods
+    // ===========================================================================
+    /**
+     * Get the context for a node (ancestors, children, references)
+     *
+     * Returns comprehensive context about a node including its containment
+     * hierarchy, children, incoming/outgoing references, type information,
+     * and relevant imports.
+     *
+     * @param nodeId - ID of the focal node
+     * @returns Context object with all related information
+     */
+    getContext(nodeId) {
+        return this.graphManager.getContext(nodeId);
+    }
+    /**
+     * Traverse the graph from a starting node
+     *
+     * Uses breadth-first search by default. Supports filtering by edge types,
+     * node types, and traversal direction.
+     *
+     * @param startId - Starting node ID
+     * @param options - Traversal options
+     * @returns Subgraph containing traversed nodes and edges
+     */
+    traverse(startId, options) {
+        return this.traverser.traverseBFS(startId, options);
+    }
+    /**
+     * Get the call graph for a function
+     *
+     * Returns both callers (functions that call this function) and
+     * callees (functions called by this function) up to the specified depth.
+     *
+     * @param nodeId - ID of the function/method node
+     * @param depth - Maximum depth in each direction (default: 2)
+     * @returns Subgraph containing the call graph
+     */
+    getCallGraph(nodeId, depth = 2) {
+        return this.traverser.getCallGraph(nodeId, depth);
+    }
+    /**
+     * Get the type hierarchy for a class/interface
+     *
+     * Returns both ancestors (types this extends/implements) and
+     * descendants (types that extend/implement this).
+     *
+     * @param nodeId - ID of the class/interface node
+     * @returns Subgraph containing the type hierarchy
+     */
+    getTypeHierarchy(nodeId) {
+        return this.traverser.getTypeHierarchy(nodeId);
+    }
+    /**
+     * Find all usages of a symbol
+     *
+     * Returns all nodes that reference the specified symbol through
+     * any edge type (calls, references, type_of, etc.).
+     *
+     * @param nodeId - ID of the symbol node
+     * @returns Array of nodes and edges that reference this symbol
+     */
+    findUsages(nodeId) {
+        return this.traverser.findUsages(nodeId);
+    }
+    /**
+     * Get callers of a function/method
+     *
+     * @param nodeId - ID of the function/method node
+     * @param maxDepth - Maximum depth to traverse (default: 1)
+     * @returns Array of nodes that call this function
+     */
+    getCallers(nodeId, maxDepth = 1) {
+        return this.traverser.getCallers(nodeId, maxDepth);
+    }
+    /**
+     * Get callees of a function/method
+     *
+     * @param nodeId - ID of the function/method node
+     * @param maxDepth - Maximum depth to traverse (default: 1)
+     * @returns Array of nodes called by this function
+     */
+    getCallees(nodeId, maxDepth = 1) {
+        return this.traverser.getCallees(nodeId, maxDepth);
+    }
+    /**
+     * Calculate the impact radius of a node
+     *
+     * Returns all nodes that could be affected by changes to this node.
+     *
+     * @param nodeId - ID of the node
+     * @param maxDepth - Maximum depth to traverse (default: 3)
+     * @returns Subgraph containing potentially impacted nodes
+     */
+    getImpactRadius(nodeId, maxDepth = 3) {
+        return this.traverser.getImpactRadius(nodeId, maxDepth);
+    }
+    /**
+     * Find the shortest path between two nodes
+     *
+     * @param fromId - Starting node ID
+     * @param toId - Target node ID
+     * @param edgeKinds - Edge types to consider (all if empty)
+     * @returns Array of nodes and edges forming the path, or null if no path exists
+     */
+    findPath(fromId, toId, edgeKinds) {
+        return this.traverser.findPath(fromId, toId, edgeKinds);
+    }
+    /**
+     * Get ancestors of a node in the containment hierarchy
+     *
+     * @param nodeId - ID of the node
+     * @returns Array of ancestor nodes from immediate parent to root
+     */
+    getAncestors(nodeId) {
+        return this.traverser.getAncestors(nodeId);
+    }
+    /**
+     * Get immediate children of a node
+     *
+     * @param nodeId - ID of the node
+     * @returns Array of child nodes
+     */
+    getChildren(nodeId) {
+        return this.traverser.getChildren(nodeId);
+    }
+    /**
+     * Get dependencies of a file
+     *
+     * @param filePath - Path to the file
+     * @returns Array of file paths this file depends on
+     */
+    getFileDependencies(filePath) {
+        return this.graphManager.getFileDependencies(filePath);
+    }
+    /**
+     * Get dependents of a file
+     *
+     * @param filePath - Path to the file
+     * @returns Array of file paths that depend on this file
+     */
+    getFileDependents(filePath) {
+        return this.graphManager.getFileDependents(filePath);
+    }
+    /**
+     * Find circular dependencies in the codebase
+     *
+     * @returns Array of cycles, each cycle is an array of file paths
+     */
+    findCircularDependencies() {
+        return this.graphManager.findCircularDependencies();
+    }
+    /**
+     * Find dead code (unreferenced symbols)
+     *
+     * @param kinds - Node kinds to check (default: functions, methods, classes)
+     * @returns Array of unreferenced nodes
+     */
+    findDeadCode(kinds) {
+        return this.graphManager.findDeadCode(kinds);
+    }
+    /**
+     * Get complexity metrics for a node
+     *
+     * @param nodeId - ID of the node
+     * @returns Object containing various complexity metrics
+     */
+    getNodeMetrics(nodeId) {
+        return this.graphManager.getNodeMetrics(nodeId);
+    }
+    // ===========================================================================
+    // Context Building
+    // ===========================================================================
+    /**
+     * Get the source code for a node
+     *
+     * Reads the file and extracts the code between startLine and endLine.
+     *
+     * @param nodeId - ID of the node
+     * @returns Code string or null if not found
+     */
+    async getCode(nodeId) {
+        return this.contextBuilder.getCode(nodeId);
+    }
+    /**
+     * Find relevant subgraph for a query
+     *
+     * Combines semantic search with graph traversal to find the most
+     * relevant nodes and their relationships for a given query.
+     *
+     * @param query - Natural language query describing the task
+     * @param options - Search and traversal options
+     * @returns Subgraph of relevant nodes and edges
+     */
+    async findRelevantContext(query, options) {
+        return this.contextBuilder.findRelevantContext(query, options);
+    }
+    /**
+     * Build context for a task
+     *
+     * Creates comprehensive context by:
+     * 1. Running FTS search to find entry points
+     * 2. Expanding the graph around entry points
+     * 3. Extracting code blocks for key nodes
+     * 4. Formatting output for Claude
+     *
+     * @param input - Task description (string or {title, description})
+     * @param options - Build options (maxNodes, includeCode, format, etc.)
+     * @returns TaskContext object or formatted string (markdown/JSON)
+     */
+    async buildContext(input, options) {
+        return this.contextBuilder.buildContext(input, options);
+    }
+    // ===========================================================================
+    // Database Management
+    // ===========================================================================
+    /**
+     * Optimize the database (vacuum and analyze)
+     */
+    optimize() {
+        this.db.optimize();
+    }
+    /**
+     * Clear all data from the graph
+     */
+    clear() {
+        this.queries.clear();
+    }
+    /**
+     * Alias for close() for backwards compatibility.
+     * @deprecated Use close() instead
+     */
+    destroy() {
+        this.close();
+    }
+    /**
+     * Completely remove CodeGraph from the project.
+     * This closes the database and deletes the .CodeGraph directory.
+     *
+     * WARNING: This permanently deletes all CodeGraph data for the project.
+     */
+    uninitialize() {
+        this.close();
+        (0, directory_1.removeDirectory)(this.projectRoot);
+    }
+}
+exports.CodeGraph = CodeGraph;
+// Default export
+exports.default = CodeGraph;
+//# sourceMappingURL=index.js.map