@duytransipher/gitnexus 1.4.6-sipher.0

package/dist/mcp/core/embedder.js

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+/**
+ * Embedder Module (Read-Only)
+ *
+ * Singleton factory for transformers.js embedding pipeline.
+ * For MCP, we only need to compute query embeddings, not batch embed.
+ */
+import { pipeline, env } from '@huggingface/transformers';
+// Model config
+const MODEL_ID = 'Snowflake/snowflake-arctic-embed-xs';
+const EMBEDDING_DIMS = 384;
+// Module-level state for singleton pattern
+let embedderInstance = null;
+let isInitializing = false;
+let initPromise = null;
+/**
+ * Initialize the embedding model (lazy, on first search)
+ */
+export const initEmbedder = async () => {
+    if (embedderInstance) {
+        return embedderInstance;
+    }
+    if (isInitializing && initPromise) {
+        return initPromise;
+    }
+    isInitializing = true;
+    initPromise = (async () => {
+        try {
+            env.allowLocalModels = false;
+            console.error('GitNexus: Loading embedding model (first search may take a moment)...');
+            // Try GPU first (DirectML on Windows, CUDA on Linux), fall back to CPU
+            const isWindows = process.platform === 'win32';
+            const gpuDevice = isWindows ? 'dml' : 'cuda';
+            const devicesToTry = [gpuDevice, 'cpu'];
+            for (const device of devicesToTry) {
+                try {
+                    // Silence stdout and stderr during model load — ONNX Runtime and transformers.js
+                    // may write progress/init messages that corrupt MCP stdio protocol or produce
+                    // noisy warnings (e.g. node assignment to execution providers).
+                    const origStdout = process.stdout.write;
+                    const origStderr = process.stderr.write;
+                    process.stdout.write = (() => true);
+                    process.stderr.write = (() => true);
+                    try {
+                        embedderInstance = await pipeline('feature-extraction', MODEL_ID, {
+                            device: device,
+                            dtype: 'fp32',
+                        });
+                    }
+                    finally {
+                        process.stdout.write = origStdout;
+                        process.stderr.write = origStderr;
+                    }
+                    console.error(`GitNexus: Embedding model loaded (${device})`);
+                    return embedderInstance;
+                }
+                catch {
+                    if (device === 'cpu')
+                        throw new Error('Failed to load embedding model');
+                }
+            }
+            throw new Error('No suitable device found');
+        }
+        catch (error) {
+            isInitializing = false;
+            initPromise = null;
+            embedderInstance = null;
+            throw error;
+        }
+        finally {
+            isInitializing = false;
+        }
+    })();
+    return initPromise;
+};
+/**
+ * Check if embedder is ready
+ */
+export const isEmbedderReady = () => embedderInstance !== null;
+/**
+ * Embed a query text for semantic search
+ */
+export const embedQuery = async (query) => {
+    const embedder = await initEmbedder();
+    const result = await embedder(query, {
+        pooling: 'mean',
+        normalize: true,
+    });
+    return Array.from(result.data);
+};
+/**
+ * Get embedding dimensions
+ */
+export const getEmbeddingDims = () => EMBEDDING_DIMS;
+/**
+ * Cleanup embedder
+ */
+export const disposeEmbedder = async () => {
+    if (embedderInstance) {
+        try {
+            if ('dispose' in embedderInstance && typeof embedderInstance.dispose === 'function') {
+                await embedderInstance.dispose();
+            }
+        }
+        catch { }
+        embedderInstance = null;
+        initPromise = null;
+    }
+};

package/dist/mcp/core/lbug-adapter.d.ts

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+/**
+ * LadybugDB Adapter (Connection Pool)
+ *
+ * Manages a pool of LadybugDB databases keyed by repoId, each with
+ * multiple Connection objects for safe concurrent query execution.
+ *
+ * LadybugDB Connections are NOT thread-safe — a single Connection
+ * segfaults if concurrent .query() calls hit it simultaneously.
+ * This adapter provides a checkout/return connection pool so each
+ * concurrent query gets its own Connection from the same Database.
+ *
+ * @see https://docs.ladybugdb.com/concurrency — multiple Connections
+ * from the same Database is the officially supported concurrency pattern.
+ */
+import lbug from '@ladybugdb/core';
+/** Saved real stdout.write — used to silence LadybugDB native output without race conditions */
+export declare const realStdoutWrite: any;
+/**
+ * Initialize (or reuse) a Database + connection pool for a specific repo.
+ * Retries on lock errors (e.g., when `gitnexus analyze` is running).
+ *
+ * Concurrent calls for the same repoId are deduplicated — the second caller
+ * awaits the first's in-progress init rather than starting a redundant one.
+ */
+export declare const initLbug: (repoId: string, dbPath: string) => Promise<void>;
+/**
+ * Initialize a pool entry from a pre-existing Database object.
+ *
+ * Used in tests to avoid the writable→close→read-only cycle that crashes
+ * on macOS due to N-API destructor segfaults.  The pool adapter reuses
+ * the core adapter's writable Database instead of opening a new read-only one.
+ *
+ * The Database is registered in the shared dbCache so closeOne() decrements
+ * the refCount correctly.  If the Database is already cached (e.g. another
+ * repoId already injected it), the existing entry is reused.
+ */
+export declare function initLbugWithDb(repoId: string, existingDb: lbug.Database, dbPath: string): Promise<void>;
+export declare const executeQuery: (repoId: string, cypher: string) => Promise<any[]>;
+/**
+ * Execute a parameterized query on a specific repo's connection pool.
+ * Uses prepare/execute pattern to prevent Cypher injection.
+ */
+export declare const executeParameterized: (repoId: string, cypher: string, params: Record<string, any>) => Promise<any[]>;
+/**
+ * Close one or all repo pools.
+ * If repoId is provided, close only that repo's connections.
+ * If omitted, close all repos.
+ */
+export declare const closeLbug: (repoId?: string) => Promise<void>;
+/**
+ * Check if a specific repo's pool is active
+ */
+export declare const isLbugReady: (repoId: string) => boolean;
+/** Regex to detect write operations in user-supplied Cypher queries */
+export declare const CYPHER_WRITE_RE: RegExp;
+/** Check if a Cypher query contains write operations */
+export declare function isWriteQuery(query: string): boolean;

package/dist/mcp/core/lbug-adapter.js

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+/**
+ * LadybugDB Adapter (Connection Pool)
+ *
+ * Manages a pool of LadybugDB databases keyed by repoId, each with
+ * multiple Connection objects for safe concurrent query execution.
+ *
+ * LadybugDB Connections are NOT thread-safe — a single Connection
+ * segfaults if concurrent .query() calls hit it simultaneously.
+ * This adapter provides a checkout/return connection pool so each
+ * concurrent query gets its own Connection from the same Database.
+ *
+ * @see https://docs.ladybugdb.com/concurrency — multiple Connections
+ * from the same Database is the officially supported concurrency pattern.
+ */
+import fs from 'fs/promises';
+import lbug from '@ladybugdb/core';
+const pool = new Map();
+const dbCache = new Map();
+/** Max repos in the pool (LRU eviction) */
+const MAX_POOL_SIZE = 5;
+/** Idle timeout before closing a repo's connections */
+const IDLE_TIMEOUT_MS = 5 * 60 * 1000; // 5 minutes
+/** Max connections per repo (caps concurrent queries per repo) */
+const MAX_CONNS_PER_REPO = 8;
+let idleTimer = null;
+/** Saved real stdout.write — used to silence LadybugDB native output without race conditions */
+export const realStdoutWrite = process.stdout.write.bind(process.stdout);
+let stdoutSilenceCount = 0;
+/** True while pre-warming connections — prevents watchdog from prematurely restoring stdout */
+let preWarmActive = false;
+/**
+ * Start the idle cleanup timer (runs every 60s)
+ */
+function ensureIdleTimer() {
+    if (idleTimer)
+        return;
+    idleTimer = setInterval(() => {
+        const now = Date.now();
+        for (const [repoId, entry] of pool) {
+            if (now - entry.lastUsed > IDLE_TIMEOUT_MS && entry.checkedOut === 0) {
+                closeOne(repoId);
+            }
+        }
+    }, 60_000);
+    if (idleTimer && typeof idleTimer === 'object' && 'unref' in idleTimer) {
+        idleTimer.unref();
+    }
+}
+/**
+ * Evict the least-recently-used repo if pool is at capacity
+ */
+function evictLRU() {
+    if (pool.size < MAX_POOL_SIZE)
+        return;
+    let oldestId = null;
+    let oldestTime = Infinity;
+    for (const [id, entry] of pool) {
+        if (entry.checkedOut === 0 && entry.lastUsed < oldestTime) {
+            oldestTime = entry.lastUsed;
+            oldestId = id;
+        }
+    }
+    if (oldestId) {
+        closeOne(oldestId);
+    }
+}
+/**
+ * Remove a repo from the pool, close its connections, and release its
+ * shared Database ref.  Only closes the Database when no other repoIds
+ * reference it (refCount === 0).
+ */
+function closeOne(repoId) {
+    const entry = pool.get(repoId);
+    if (!entry)
+        return;
+    entry.closed = true;
+    // Close available connections — fire-and-forget with .catch() to prevent
+    // unhandled rejections.  Native close() returns Promise<void> but can crash
+    // the N-API destructor on macOS/Windows; deferring to process exit lets
+    // dangerouslyIgnoreUnhandledErrors absorb the crash.
+    for (const conn of entry.available) {
+        conn.close().catch(() => { });
+    }
+    entry.available.length = 0;
+    // Checked-out connections can't be closed here — they're in-flight.
+    // The checkin() function detects entry.closed and closes them on return.
+    // Only close the Database when no other repoIds reference it.
+    // External databases (injected via initLbugWithDb) are never closed here —
+    // the core adapter owns them and handles their lifecycle.
+    const shared = dbCache.get(entry.dbPath);
+    if (shared) {
+        shared.refCount--;
+        if (shared.refCount === 0) {
+            if (shared.external) {
+                // External databases are owned by the core adapter — don't close
+                // or remove from cache.  Keep the entry so future initLbug() calls
+                // for the same dbPath reuse it instead of hitting a file lock.
+                shared.refCount = 0;
+            }
+            else {
+                shared.db.close().catch(() => { });
+                dbCache.delete(entry.dbPath);
+            }
+        }
+    }
+    pool.delete(repoId);
+}
+/**
+ * Create a new Connection from a repo's Database.
+ * Silences stdout to prevent native module output from corrupting MCP stdio.
+ */
+function silenceStdout() {
+    if (stdoutSilenceCount++ === 0) {
+        process.stdout.write = (() => true);
+    }
+}
+function restoreStdout() {
+    if (--stdoutSilenceCount <= 0) {
+        stdoutSilenceCount = 0;
+        process.stdout.write = realStdoutWrite;
+    }
+}
+// Safety watchdog: restore stdout if it gets stuck silenced (e.g. native crash
+// inside createConnection before restoreStdout runs).
+setInterval(() => {
+    if (stdoutSilenceCount > 0 && !preWarmActive) {
+        stdoutSilenceCount = 0;
+        process.stdout.write = realStdoutWrite;
+    }
+}, 1000).unref();
+function createConnection(db) {
+    silenceStdout();
+    try {
+        return new lbug.Connection(db);
+    }
+    finally {
+        restoreStdout();
+    }
+}
+/** Query timeout in milliseconds */
+const QUERY_TIMEOUT_MS = 30_000;
+/** Waiter queue timeout in milliseconds */
+const WAITER_TIMEOUT_MS = 15_000;
+const LOCK_RETRY_ATTEMPTS = 3;
+const LOCK_RETRY_DELAY_MS = 2000;
+/** Deduplicates concurrent initLbug calls for the same repoId */
+const initPromises = new Map();
+/**
+ * Initialize (or reuse) a Database + connection pool for a specific repo.
+ * Retries on lock errors (e.g., when `gitnexus analyze` is running).
+ *
+ * Concurrent calls for the same repoId are deduplicated — the second caller
+ * awaits the first's in-progress init rather than starting a redundant one.
+ */
+export const initLbug = async (repoId, dbPath) => {
+    const existing = pool.get(repoId);
+    if (existing) {
+        existing.lastUsed = Date.now();
+        return;
+    }
+    // Deduplicate concurrent init calls for the same repoId —
+    // prevents double-init race when multiple parallel tool calls
+    // trigger initialization for the same repo simultaneously.
+    const pending = initPromises.get(repoId);
+    if (pending)
+        return pending;
+    const promise = doInitLbug(repoId, dbPath);
+    initPromises.set(repoId, promise);
+    try {
+        await promise;
+    }
+    finally {
+        initPromises.delete(repoId);
+    }
+};
+/**
+ * Internal init — creates DB, pre-warms connections, loads FTS, then registers pool.
+ * Pool entry is registered LAST so concurrent executeQuery calls see either
+ * "not initialized" (and throw) or a fully ready pool — never a half-built one.
+ */
+async function doInitLbug(repoId, dbPath) {
+    // Check if database exists
+    try {
+        await fs.stat(dbPath);
+    }
+    catch {
+        throw new Error(`LadybugDB not found at ${dbPath}. Run: gitnexus analyze`);
+    }
+    evictLRU();
+    // Reuse an existing native Database if another repoId already opened this path.
+    // This prevents buffer manager exhaustion from multiple mmap regions on the same file.
+    let shared = dbCache.get(dbPath);
+    if (!shared) {
+        // Open in read-only mode — MCP server never writes to the database.
+        // This allows multiple MCP server instances to read concurrently, and
+        // avoids lock conflicts when `gitnexus analyze` is writing.
+        let lastError = null;
+        for (let attempt = 1; attempt <= LOCK_RETRY_ATTEMPTS; attempt++) {
+            silenceStdout();
+            try {
+                const db = new lbug.Database(dbPath, 0, // bufferManagerSize (default)
+                false, // enableCompression (default)
+                true);
+                restoreStdout();
+                shared = { db, refCount: 0, ftsLoaded: false };
+                dbCache.set(dbPath, shared);
+                break;
+            }
+            catch (err) {
+                restoreStdout();
+                lastError = err instanceof Error ? err : new Error(String(err));
+                const isLockError = lastError.message.includes('Could not set lock')
+                    || lastError.message.includes('lock');
+                if (!isLockError || attempt === LOCK_RETRY_ATTEMPTS)
+                    break;
+                await new Promise(resolve => setTimeout(resolve, LOCK_RETRY_DELAY_MS * attempt));
+            }
+        }
+        if (!shared) {
+            throw new Error(`LadybugDB unavailable for ${repoId}. Another process may be rebuilding the index. ` +
+                `Retry later. (${lastError?.message || 'unknown error'})`);
+        }
+    }
+    shared.refCount++;
+    const db = shared.db;
+    // Pre-create the full pool upfront so createConnection() (which silences
+    // stdout) is never called lazily during active query execution.
+    // Mark preWarmActive so the watchdog timer doesn't interfere.
+    preWarmActive = true;
+    const available = [];
+    try {
+        for (let i = 0; i < MAX_CONNS_PER_REPO; i++) {
+            available.push(createConnection(db));
+        }
+    }
+    finally {
+        preWarmActive = false;
+    }
+    // Load FTS extension once per shared Database.
+    // Done BEFORE pool registration so no concurrent checkout can grab
+    // the connection while the async FTS load is in progress.
+    if (!shared.ftsLoaded) {
+        try {
+            await available[0].query('LOAD EXTENSION fts');
+            shared.ftsLoaded = true;
+        }
+        catch {
+            // Extension may not be installed — FTS queries will fail gracefully
+        }
+    }
+    // Register pool entry only after all connections are pre-warmed and FTS is
+    // loaded.  Concurrent executeQuery calls see either "not initialized"
+    // (and throw cleanly) or a fully ready pool — never a half-built one.
+    pool.set(repoId, { db, available, checkedOut: 0, waiters: [], lastUsed: Date.now(), dbPath, closed: false });
+    ensureIdleTimer();
+}
+/**
+ * Initialize a pool entry from a pre-existing Database object.
+ *
+ * Used in tests to avoid the writable→close→read-only cycle that crashes
+ * on macOS due to N-API destructor segfaults.  The pool adapter reuses
+ * the core adapter's writable Database instead of opening a new read-only one.
+ *
+ * The Database is registered in the shared dbCache so closeOne() decrements
+ * the refCount correctly.  If the Database is already cached (e.g. another
+ * repoId already injected it), the existing entry is reused.
+ */
+export async function initLbugWithDb(repoId, existingDb, dbPath) {
+    const existing = pool.get(repoId);
+    if (existing) {
+        existing.lastUsed = Date.now();
+        return;
+    }
+    // Register in dbCache with external: true so other initLbug() calls
+    // for the same dbPath reuse this Database instead of trying to open
+    // a new one (which would fail with a file lock error).
+    // closeOne() respects the external flag and skips db.close().
+    let shared = dbCache.get(dbPath);
+    if (!shared) {
+        shared = { db: existingDb, refCount: 0, ftsLoaded: false, external: true };
+        dbCache.set(dbPath, shared);
+    }
+    shared.refCount++;
+    const available = [];
+    preWarmActive = true;
+    try {
+        for (let i = 0; i < MAX_CONNS_PER_REPO; i++) {
+            available.push(createConnection(existingDb));
+        }
+    }
+    finally {
+        preWarmActive = false;
+    }
+    // Load FTS extension if not already loaded on this Database
+    try {
+        await available[0].query('LOAD EXTENSION fts');
+    }
+    catch {
+        // Extension may already be loaded or not installed
+    }
+    pool.set(repoId, {
+        db: existingDb,
+        available,
+        checkedOut: 0,
+        waiters: [],
+        lastUsed: Date.now(),
+        dbPath,
+        closed: false
+    });
+    ensureIdleTimer();
+}
+/**
+ * Checkout a connection from the pool.
+ * Returns an available connection, or creates a new one if under the cap.
+ * If all connections are busy and at cap, queues the caller until one is returned.
+ */
+function checkout(entry) {
+    // Fast path: grab an available connection
+    if (entry.available.length > 0) {
+        entry.checkedOut++;
+        return Promise.resolve(entry.available.pop());
+    }
+    // Pool was pre-warmed to MAX_CONNS_PER_REPO during init.  If we're here
+    // with fewer total connections, something leaked — surface the bug rather
+    // than silently creating a connection (which would silence stdout mid-query).
+    const totalConns = entry.available.length + entry.checkedOut;
+    if (totalConns < MAX_CONNS_PER_REPO) {
+        throw new Error(`Connection pool integrity error: expected ${MAX_CONNS_PER_REPO} ` +
+            `connections but found ${totalConns} (${entry.available.length} available, ` +
+            `${entry.checkedOut} checked out)`);
+    }
+    // At capacity — queue the caller with a timeout.
+    return new Promise((resolve, reject) => {
+        const waiter = (conn) => {
+            clearTimeout(timer);
+            resolve(conn);
+        };
+        const timer = setTimeout(() => {
+            const idx = entry.waiters.indexOf(waiter);
+            if (idx !== -1)
+                entry.waiters.splice(idx, 1);
+            reject(new Error(`Connection pool exhausted: timed out after ${WAITER_TIMEOUT_MS}ms waiting for a free connection`));
+        }, WAITER_TIMEOUT_MS);
+        entry.waiters.push(waiter);
+    });
+}
+/**
+ * Return a connection to the pool after use.
+ * If the pool entry was closed while the connection was checked out (e.g.
+ * LRU eviction), close the orphaned connection instead of returning it.
+ * If there are queued waiters, hand the connection directly to the next one
+ * instead of putting it back in the available array (avoids race conditions).
+ */
+function checkin(entry, conn) {
+    if (entry.closed) {
+        // Pool entry was deleted during checkout — close the orphaned connection
+        conn.close().catch(() => { });
+        return;
+    }
+    if (entry.waiters.length > 0) {
+        // Hand directly to the next waiter — no intermediate available state
+        const waiter = entry.waiters.shift();
+        waiter(conn);
+    }
+    else {
+        entry.checkedOut--;
+        entry.available.push(conn);
+    }
+}
+/**
+ * Execute a query on a specific repo's connection pool.
+ * Automatically checks out a connection, runs the query, and returns it.
+ */
+/** Race a promise against a timeout */
+function withTimeout(promise, ms, label) {
+    let timer;
+    const timeout = new Promise((_, reject) => {
+        timer = setTimeout(() => reject(new Error(`${label} timed out after ${ms}ms`)), ms);
+    });
+    return Promise.race([promise, timeout]).finally(() => clearTimeout(timer));
+}
+export const executeQuery = async (repoId, cypher) => {
+    const entry = pool.get(repoId);
+    if (!entry) {
+        throw new Error(`LadybugDB not initialized for repo "${repoId}". Call initLbug first.`);
+    }
+    if (isWriteQuery(cypher)) {
+        throw new Error('Write operations are not allowed. The pool adapter is read-only.');
+    }
+    entry.lastUsed = Date.now();
+    const conn = await checkout(entry);
+    try {
+        const queryResult = await withTimeout(conn.query(cypher), QUERY_TIMEOUT_MS, 'Query');
+        const result = Array.isArray(queryResult) ? queryResult[0] : queryResult;
+        const rows = await result.getAll();
+        return rows;
+    }
+    finally {
+        checkin(entry, conn);
+    }
+};
+/**
+ * Execute a parameterized query on a specific repo's connection pool.
+ * Uses prepare/execute pattern to prevent Cypher injection.
+ */
+export const executeParameterized = async (repoId, cypher, params) => {
+    const entry = pool.get(repoId);
+    if (!entry) {
+        throw new Error(`LadybugDB not initialized for repo "${repoId}". Call initLbug first.`);
+    }
+    entry.lastUsed = Date.now();
+    const conn = await checkout(entry);
+    try {
+        const stmt = await withTimeout(conn.prepare(cypher), QUERY_TIMEOUT_MS, 'Prepare');
+        if (!stmt.isSuccess()) {
+            const errMsg = await stmt.getErrorMessage();
+            throw new Error(`Prepare failed: ${errMsg}`);
+        }
+        const queryResult = await withTimeout(conn.execute(stmt, params), QUERY_TIMEOUT_MS, 'Execute');
+        const result = Array.isArray(queryResult) ? queryResult[0] : queryResult;
+        const rows = await result.getAll();
+        return rows;
+    }
+    finally {
+        checkin(entry, conn);
+    }
+};
+/**
+ * Close one or all repo pools.
+ * If repoId is provided, close only that repo's connections.
+ * If omitted, close all repos.
+ */
+export const closeLbug = async (repoId) => {
+    if (repoId) {
+        closeOne(repoId);
+        return;
+    }
+    for (const id of [...pool.keys()]) {
+        closeOne(id);
+    }
+    if (idleTimer) {
+        clearInterval(idleTimer);
+        idleTimer = null;
+    }
+};
+/**
+ * Check if a specific repo's pool is active
+ */
+export const isLbugReady = (repoId) => pool.has(repoId);
+/** Regex to detect write operations in user-supplied Cypher queries */
+export const CYPHER_WRITE_RE = /\b(CREATE|DELETE|SET|MERGE|REMOVE|DROP|ALTER|COPY|DETACH)\b/i;
+/** Check if a Cypher query contains write operations */
+export function isWriteQuery(query) {
+    return CYPHER_WRITE_RE.test(query);
+}