codetree-claude 1.5.3 → 1.5.6

package/dist/indexer/indexer.d.ts

@@ -54,6 +54,40 @@ export declare class Indexer {
     filesContainingAll(rawTokens: string[]): Set<string>;
     /** Whether the postings index has data for any of these tokens (heuristic for "warm"). */
     postingsAvailableFor(rawTokens: string[]): boolean;
+    /**
+     * Split a free-form query string into the same identifier tokens the indexer
+     * stores in its postings (lowercased, ≥3 chars). Used by probe / content
+     * search so a multi-word query like "fast-growing startups" can still be
+     * narrowed via postings (was previously looked up as a single literal key
+     * which never existed, forcing an alphabetically-bounded fallback that
+     * silently missed any file past the first MAX_FALLBACK_FILES).
+     */
+    tokenizeQuery(query: string): string[];
+    /**
+     * Return the set of files that the postings index says might contain the
+     * given query, or null when postings cannot answer (no indexable subtokens).
+     * Caller must treat null as "I don't know — please fall back to a scan."
+     *
+     * Intersects when multiple subtokens exist (most selective). If intersection
+     * is empty, relaxes to union (handles the case where one rare subtoken
+     * isn't in postings at all but others are).
+     */
+    filesContainingQuery(query: string): Set<string> | null;
+    /**
+     * Safety-net: a cheap incremental rescan that walks the project tree and
+     * calls indexFile on every file. Files whose (size, mtime) match the index
+     * short-circuit immediately, so the cost is roughly one statSync per file —
+     * fast enough to run on a timer (e.g. every 10 min) as belt-and-suspenders
+     * against missed chokidar events on Windows / OneDrive / network drives.
+     *
+     * Does nothing if a full scan is already in progress.
+     */
+    safetyNetRescan(): Promise<{
+        scanned: number;
+        reindexed: number;
+        pruned: number;
+        ms: number;
+    } | null>;
     /**
      * Invalidate all in-memory caches without deleting indexed data.
      * Used after branch switches — forces mtime revalidation on next file access.

package/dist/indexer/indexer.d.ts.map

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

@@ -342,6 +342,86 @@ export class Indexer {
         }
         return false;
     }
+    /**
+     * Split a free-form query string into the same identifier tokens the indexer
+     * stores in its postings (lowercased, ≥3 chars). Used by probe / content
+     * search so a multi-word query like "fast-growing startups" can still be
+     * narrowed via postings (was previously looked up as a single literal key
+     * which never existed, forcing an alphabetically-bounded fallback that
+     * silently missed any file past the first MAX_FALLBACK_FILES).
+     */
+    tokenizeQuery(query) {
+        const out = [];
+        if (!query)
+            return out;
+        const re = /[A-Za-z_][A-Za-z0-9_]{2,}/g;
+        let m;
+        const seen = new Set();
+        while ((m = re.exec(query)) !== null) {
+            const t = m[0].toLowerCase();
+            if (t.length >= 3 && t.length <= 64 && !seen.has(t)) {
+                seen.add(t);
+                out.push(t);
+            }
+        }
+        return out;
+    }
+    /**
+     * Return the set of files that the postings index says might contain the
+     * given query, or null when postings cannot answer (no indexable subtokens).
+     * Caller must treat null as "I don't know — please fall back to a scan."
+     *
+     * Intersects when multiple subtokens exist (most selective). If intersection
+     * is empty, relaxes to union (handles the case where one rare subtoken
+     * isn't in postings at all but others are).
+     */
+    filesContainingQuery(query) {
+        const subtokens = this.tokenizeQuery(query);
+        if (subtokens.length === 0)
+            return null;
+        if (subtokens.length === 1) {
+            const set = this.tokenPostings.get(subtokens[0]);
+            return set ? new Set(set) : null;
+        }
+        const intersection = this.filesContainingAll(subtokens);
+        if (intersection.size > 0)
+            return intersection;
+        const union = this.filesContainingAny(subtokens);
+        return union.size > 0 ? union : null;
+    }
+    /**
+     * Safety-net: a cheap incremental rescan that walks the project tree and
+     * calls indexFile on every file. Files whose (size, mtime) match the index
+     * short-circuit immediately, so the cost is roughly one statSync per file —
+     * fast enough to run on a timer (e.g. every 10 min) as belt-and-suspenders
+     * against missed chokidar events on Windows / OneDrive / network drives.
+     *
+     * Does nothing if a full scan is already in progress.
+     */
+    async safetyNetRescan() {
+        if (this.indexing)
+            return null;
+        const start = Date.now();
+        const filePaths = this.collectFiles(this.config.projectRoot);
+        let reindexed = 0;
+        for (const absPath of filePaths) {
+            try {
+                const result = this.indexFile(absPath);
+                if (result)
+                    reindexed++;
+            }
+            catch { /* per-file errors shouldn't break the sweep */ }
+        }
+        const beforePrune = this.db.getFileCount();
+        this.pruneDeletedFiles(filePaths);
+        const afterPrune = this.db.getFileCount();
+        return {
+            scanned: filePaths.length,
+            reindexed,
+            pruned: Math.max(0, beforePrune - afterPrune),
+            ms: Date.now() - start,
+        };
+    }
     /**
      * Invalidate all in-memory caches without deleting indexed data.
      * Used after branch switches — forces mtime revalidation on next file access.

package/dist/indexer/indexer.js.map

@@ -1 +1 @@
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package/dist/indexer/watcher.d.ts

@@ -7,9 +7,13 @@ export declare class FileWatcher {
     private indexer;
     private debounceTimers;
     private branchRescanTimer;
+    private safetyTimer;
+    private safetyInFlight;
     private running;
     constructor(config: CodeTreeConfig, indexer: Indexer);
     start(): void;
+    private scheduleSafetyRescan;
+    private runSafetyRescan;
     private startGitWatcher;
     stop(): void;
     isRunning(): boolean;

package/dist/indexer/watcher.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../../src/indexer/watcher.ts"],"names":[],"mappings":"AAGA,OAAO,EAAiB,KAAK,cAAc,EAAE,MAAM,cAAc,CAAC;AAClE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAE5C,qBAAa,WAAW;IACtB,OAAO,CAAC,OAAO,CAA0B;IACzC,OAAO,CAAC,UAAU,CAA0B;IAC5C,OAAO,CAAC,MAAM,CAAiB;IAC/B,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,cAAc,CAAyD;IAC/E,OAAO,CAAC,iBAAiB,CAA8C;IACvE,OAAO,CAAC,OAAO,CAAS;gBAEZ,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO;IAKpD,KAAK,IAAI,IAAI;IA+Bb,OAAO,CAAC,eAAe;IAoBvB,IAAI,IAAI,IAAI;IAoBZ,SAAS,IAAI,OAAO;IAIpB,OAAO,CAAC,YAAY;IAqBpB,OAAO,CAAC,YAAY;CAQrB"}
+{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../../src/indexer/watcher.ts"],"names":[],"mappings":"AAGA,OAAO,EAAiB,KAAK,cAAc,EAAE,MAAM,cAAc,CAAC;AAClE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAY5C,qBAAa,WAAW;IACtB,OAAO,CAAC,OAAO,CAA0B;IACzC,OAAO,CAAC,UAAU,CAA0B;IAC5C,OAAO,CAAC,MAAM,CAAiB;IAC/B,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,cAAc,CAAyD;IAC/E,OAAO,CAAC,iBAAiB,CAA8C;IACvE,OAAO,CAAC,WAAW,CAA8C;IACjE,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,OAAO,CAAS;gBAEZ,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO;IAKpD,KAAK,IAAI,IAAI;IA4Cb,OAAO,CAAC,oBAAoB;YAYd,eAAe;IAmB7B,OAAO,CAAC,eAAe;IAwBvB,IAAI,IAAI,IAAI;IAwBZ,SAAS,IAAI,OAAO;IAIpB,OAAO,CAAC,YAAY;IAqBpB,OAAO,CAAC,YAAY;CAQrB"}

package/dist/indexer/watcher.js

@@ -2,6 +2,15 @@ import chokidar from "chokidar";
 import { resolve, join } from "node:path";
 import { existsSync } from "node:fs";
 import { normalizePath } from "../config.js";
+// Periodic safety-net rescan interval. chokidar can miss events on Windows
+// (cross-drive moves, OneDrive sync hiccups, network drives), so we sweep
+// the tree at this cadence with a cheap mtime-based incremental rescan.
+// Every file already-current short-circuits in indexFile() via quickHash,
+// so a no-op sweep on a 2k-file repo is well under a second.
+const SAFETY_RESCAN_INTERVAL_MS = 10 * 60 * 1000; // 10 min
+// First safety-net sweep runs sooner so a freshly-restarted server catches
+// any edits made between shutdown and startup without waiting 10 min.
+const SAFETY_RESCAN_FIRST_MS = 60 * 1000; // 1 min
 export class FileWatcher {
     watcher = null;
     gitWatcher = null;
@@ -9,6 +18,8 @@ export class FileWatcher {
     indexer;
     debounceTimers = new Map();
     branchRescanTimer = null;
+    safetyTimer = null;
+    safetyInFlight = false;
     running = false;
     constructor(config, indexer) {
         this.config = config;
@@ -29,17 +40,61 @@ export class FileWatcher {
             ignoreInitial: true,
             usePolling: this.config.watch.usePolling,
             awaitWriteFinish: {
-                stabilityThreshold: 200,
+                // Slightly more generous than before — OneDrive/Dropbox sync can hold
+                // a file open for >200ms, leading to half-written reads.
+                stabilityThreshold: 400,
                 pollInterval: 100,
             },
         });
         this.watcher.on("change", (path) => this.handleChange(path));
         this.watcher.on("add", (path) => this.handleChange(path));
         this.watcher.on("unlink", (path) => this.handleDelete(path));
+        // Without this handler, chokidar errors (EMFILE, ENOSPC inotify limit,
+        // network drive disconnect) crash silently and the index goes stale with
+        // no log line. We surface them and let the safety-net sweep keep things
+        // mostly current.
+        this.watcher.on("error", (err) => {
+            console.error(`[codetree] File watcher error:`, err);
+        });
         // Watch .git/HEAD for branch switches (git checkout, git switch)
         this.startGitWatcher();
+        // Belt-and-suspenders: periodic incremental rescan in case chokidar
+        // missed any events (Windows / OneDrive / network drives are notorious).
+        this.scheduleSafetyRescan(SAFETY_RESCAN_FIRST_MS);
         this.running = true;
     }
+    scheduleSafetyRescan(delayMs) {
+        if (this.safetyTimer)
+            clearTimeout(this.safetyTimer);
+        this.safetyTimer = setTimeout(() => {
+            this.safetyTimer = null;
+            this.runSafetyRescan().finally(() => {
+                // Only schedule the next sweep if we're still running — don't
+                // resurrect the timer after stop().
+                if (this.running)
+                    this.scheduleSafetyRescan(SAFETY_RESCAN_INTERVAL_MS);
+            });
+        }, delayMs);
+    }
+    async runSafetyRescan() {
+        if (this.safetyInFlight)
+            return;
+        this.safetyInFlight = true;
+        try {
+            const result = await this.indexer.safetyNetRescan();
+            if (result && (result.reindexed > 0 || result.pruned > 0)) {
+                console.error(`[codetree] Safety-net rescan: ${result.scanned} scanned, ` +
+                    `${result.reindexed} reindexed, ${result.pruned} pruned in ${result.ms}ms ` +
+                    `(chokidar missed events — investigate if frequent).`);
+            }
+        }
+        catch (err) {
+            console.error(`[codetree] Safety-net rescan failed:`, err);
+        }
+        finally {
+            this.safetyInFlight = false;
+        }
+    }
     startGitWatcher() {
         const gitHead = join(this.config.projectRoot, ".git", "HEAD");
         if (!existsSync(gitHead))
@@ -48,6 +103,9 @@ export class FileWatcher {
             persistent: true,
             ignoreInitial: true,
         });
+        this.gitWatcher.on("error", (err) => {
+            console.error(`[codetree] Git HEAD watcher error:`, err);
+        });
         this.gitWatcher.on("change", () => {
             // Debounce: git operations may touch HEAD multiple times
             if (this.branchRescanTimer)
@@ -72,6 +130,10 @@ export class FileWatcher {
             clearTimeout(this.branchRescanTimer);
             this.branchRescanTimer = null;
         }
+        if (this.safetyTimer) {
+            clearTimeout(this.safetyTimer);
+            this.safetyTimer = null;
+        }
         for (const timer of this.debounceTimers.values()) {
             clearTimeout(timer);
         }

package/dist/indexer/watcher.js.map

@@ -1 +1 @@
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package/dist/server/ipc.d.ts

@@ -22,10 +22,20 @@ export declare class IpcServer {
      */
     private probeCodetreeServer;
     /**
-     * If a stale codetree process is holding our target port, kill it.
-     * Only kills processes that are confirmed stale codetree servers (not arbitrary processes).
+     * If a dead/zombie codetree process is holding our target port, kill it.
+     * Safety: only kills processes that match our project's recorded PID
+     * (from .codetree/ipc.port) — never kills arbitrary processes.
      */
     private freeZombiePort;
+    /**
+     * Find PID of process listening on the given port. Returns null if none found.
+     */
+    private findPidOnPort;
+    /**
+     * Check if the given port is the deterministic port for this project.
+     * If so, we own it and can safely kill zombies on it.
+     */
+    private isDeterministicPortForUs;
     getPort(): number;
     /**
      * True if this instance owns the IPC server process (we bound the port).

package/dist/server/ipc.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ipc.d.ts","sourceRoot":"","sources":["../../src/server/ipc.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AACrD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAEvD,OAAO,EAAiB,KAAK,cAAc,EAAE,MAAM,cAAc,CAAC;AAclE;;;GAGG;AACH,qBAAa,SAAS;IACpB,OAAO,CAAC,MAAM,CAAuB;IACrC,OAAO,CAAC,IAAI,CAAK;IACjB,OAAO,CAAC,MAAM,CAAiB;IAC/B,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,EAAE,CAAW;IACrB,OAAO,CAAC,WAAW,CAAc;IAGjC,OAAO,CAAC,KAAK,CAKX;gBAEU,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ;IAQ5D,KAAK,IAAI,OAAO,CAAC,MAAM,CAAC;IA8F9B;;;;OAIG;IACH,OAAO,CAAC,mBAAmB;IA0C3B;;;;OAIG;YACW,cAAc;IAsD5B;;OAEG;IACH,OAAO,CAAC,aAAa;IA8BrB;;;OAGG;IACH,OAAO,CAAC,wBAAwB;IAQhC,OAAO,IAAI,MAAM;IAIjB;;;OAGG;IACH,OAAO,IAAI,OAAO;IAIlB,IAAI,IAAI,IAAI;IAUZ,OAAO,CAAC,aAAa;IAQrB;;OAEG;IACH,OAAO,CAAC,QAAQ;YAiBF,aAAa;IA8E3B;;;OAGG;IACH,OAAO,CAAC,WAAW;IAgDnB;;OAEG;IACH,OAAO,CAAC,iBAAiB;IA6BzB;;OAEG;IACH,OAAO,CAAC,eAAe;IA0BvB,OAAO,CAAC,YAAY;IAWpB,OAAO,CAAC,WAAW;IAanB,OAAO,CAAC,mBAAmB;IAY3B,OAAO,CAAC,oBAAoB;IAe5B,OAAO,CAAC,sBAAsB;IAY9B,OAAO,CAAC,sBAAsB;IAY9B,OAAO,CAAC,oBAAoB;IAY5B,OAAO,CAAC,oBAAoB;IAwB5B,OAAO,CAAC,gBAAgB;IAqBxB,OAAO,CAAC,oBAAoB;IA6C5B,OAAO,CAAC,uBAAuB;IA2C/B;;OAEG;IACH,OAAO,CAAC,aAAa;IAYrB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,gBAAgB;IAmCxB,OAAO,CAAC,YAAY;CAWrB"}

package/dist/server/ipc.js

@@ -1,7 +1,8 @@
 import { createServer, request as httpRequest } from "node:http";
-import { writeFileSync, mkdirSync, existsSync } from "node:fs";
+import { writeFileSync, mkdirSync, existsSync, readFileSync } from "node:fs";
 import { dirname, join } from "node:path";
 import { createHash } from "node:crypto";
+import { execSync } from "node:child_process";
 import { DiskManager } from "../storage/disk-manager.js";
 import { normalizePath } from "../config.js";
 import { relative } from "node:path";
@@ -102,8 +103,11 @@ export class IpcServer {
                 }
                 if (attempt < RETRY_DELAYS_MS.length) {
                     const delay = RETRY_DELAYS_MS[attempt];
-                    process.stderr.write(`[codetree] Port ${targetPort} EADDRINUSE; retrying in ${delay}ms ` +
+                    process.stderr.write(`[codetree] Port ${targetPort} EADDRINUSE; attempting zombie kill and retrying in ${delay}ms ` +
                         `(attempt ${attempt + 1}/${RETRY_DELAYS_MS.length}).\n`);
+                    // Try to kill zombie again on each retry — the process may have become unresponsive
+                    // between retries, or our first kill attempt may have failed silently.
+                    await this.freeZombiePort(targetPort);
                     await new Promise((r) => setTimeout(r, delay));
                 }
             }
@@ -163,40 +167,102 @@ export class IpcServer {
         });
     }
     /**
-     * If a stale codetree process is holding our target port, kill it.
-     * Only kills processes that are confirmed stale codetree servers (not arbitrary processes).
+     * If a dead/zombie codetree process is holding our target port, kill it.
+     * Safety: only kills processes that match our project's recorded PID
+     * (from .codetree/ipc.port) — never kills arbitrary processes.
      */
     async freeZombiePort(port) {
-        // First, check if anything on this port responds as a codetree server
-        // If it does but for a different project, we should NOT kill it — just fall back to auto-port
+        // First, check if anything on this port responds as a healthy codetree server
         const isCodetree = await this.probeCodetreeServer(port);
         if (isCodetree) {
-            // It's a live codetree for our project — handled by caller (singleton reuse)
+            // Live codetree — caller handles singleton reuse
             return;
         }
-        // Check if port is in use at all by trying a quick probe
-        const isInUse = await new Promise((resolve) => {
-            const timer = setTimeout(() => resolve(false), 300);
-            try {
-                const req = httpRequest({ hostname: "127.0.0.1", port, path: "/", method: "GET", timeout: 300 }, () => { clearTimeout(timer); resolve(true); });
-                req.on("error", (err) => {
-                    clearTimeout(timer);
-                    // ECONNREFUSED means port is free
-                    resolve(err.code !== "ECONNREFUSED");
-                });
-                req.on("timeout", () => { req.destroy(); clearTimeout(timer); resolve(false); });
-                req.end();
+        // Find the PID holding the port
+        const zombiePid = this.findPidOnPort(port);
+        if (!zombiePid)
+            return; // Port is free, nothing to do
+        // Read our project's recorded PID (if any) — this is the only PID we're allowed to kill
+        const portFile = join(this.config.projectRoot, ".codetree", "ipc.port");
+        let recordedPid = null;
+        try {
+            if (existsSync(portFile)) {
+                const content = readFileSync(portFile, "utf-8").trim();
+                // Format: "PORT" or "PORT:PID"
+                const parts = content.split(":");
+                if (parts.length >= 2)
+                    recordedPid = parseInt(parts[1], 10) || null;
             }
-            catch {
-                clearTimeout(timer);
-                resolve(false);
+        }
+        catch { /* ignore */ }
+        // Safety check: only kill if the zombie PID matches our recorded PID
+        // OR if the port is the deterministic port for this project (which codetree itself chose)
+        const isOurZombie = recordedPid === zombiePid || this.isDeterministicPortForUs(port);
+        if (!isOurZombie) {
+            process.stderr.write(`[codetree] Port ${port} held by PID ${zombiePid} — not ours, skipping kill.\n`);
+            return;
+        }
+        // Kill the zombie
+        try {
+            if (process.platform === "win32") {
+                execSync(`taskkill /F /PID ${zombiePid}`, { stdio: "ignore" });
             }
-        });
-        if (!isInUse)
-            return; // Port is free, nothing to do
-        // Port is held by a non-codetree process or a codetree for a different project.
-        // Do NOT kill it — the caller will fall back to auto-assigned port.
-        process.stderr.write(`[codetree] Port ${port} in use by another process. Will use auto-assigned port.\n`);
+            else {
+                execSync(`kill -9 ${zombiePid}`, { stdio: "ignore" });
+            }
+            process.stderr.write(`[codetree] Killed zombie codetree process ${zombiePid} holding port ${port}.\n`);
+            // Give OS time to release the socket
+            await new Promise((r) => setTimeout(r, 500));
+        }
+        catch (err) {
+            process.stderr.write(`[codetree] Failed to kill zombie PID ${zombiePid}: ${err.message}\n`);
+        }
+    }
+    /**
+     * Find PID of process listening on the given port. Returns null if none found.
+     */
+    findPidOnPort(port) {
+        try {
+            const isWindows = process.platform === "win32";
+            let output;
+            if (isWindows) {
+                // netstat: look for LISTENING on our port
+                output = execSync(`netstat -ano`, { encoding: "utf-8", stdio: ["pipe", "pipe", "ignore"] });
+                const lines = output.split("\n");
+                for (const line of lines) {
+                    if (line.includes(`127.0.0.1:${port}`) && line.includes("LISTENING")) {
+                        const parts = line.trim().split(/\s+/);
+                        const pid = parseInt(parts[parts.length - 1], 10);
+                        if (pid && pid !== process.pid)
+                            return pid;
+                    }
+                }
+            }
+            else {
+                // lsof on Unix/Mac
+                output = execSync(`lsof -i :${port} -t -s TCP:LISTEN`, {
+                    encoding: "utf-8",
+                    stdio: ["pipe", "pipe", "ignore"],
+                });
+                const pid = parseInt(output.trim().split("\n")[0], 10);
+                if (pid && pid !== process.pid)
+                    return pid;
+            }
+        }
+        catch {
+            // Command failed (e.g., port not in use)
+        }
+        return null;
+    }
+    /**
+     * Check if the given port is the deterministic port for this project.
+     * If so, we own it and can safely kill zombies on it.
+     */
+    isDeterministicPortForUs(port) {
+        const hash = createHash("sha256").update(this.config.projectRoot.toLowerCase()).digest();
+        const offset = ((hash[0] << 8) | hash[1]) % 1000;
+        const deterministicPort = 47000 + offset;
+        return port === deterministicPort;
     }
     getPort() {
         return this.port;
@@ -222,7 +288,8 @@ export class IpcServer {
         const dir = dirname(portFilePath);
         if (!existsSync(dir))
             mkdirSync(dir, { recursive: true });
-        writeFileSync(portFilePath, String(this.port), "utf-8");
+        // Format: PORT:PID — PID enables safe zombie detection on next startup
+        writeFileSync(portFilePath, `${this.port}:${process.pid}`, "utf-8");
     }
     /**
      * Read the full request body as a string (for POST requests with JSON body).

package/dist/server/ipc.js.map

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package/dist/server/mcp-server.js

@@ -164,17 +164,40 @@ async function main() {
     const transport = new StdioServerTransport();
     await server.connect(transport);
     logToStderr("[codetree] MCP server connected via stdio");
-    // Graceful shutdown
-    const shutdown = () => {
-        logToStderr("[codetree] Shutting down...");
-        watcher?.stop();
-        ipc.stop();
-        db.close();
+    // Graceful shutdown — must release the deterministic IPC port quickly so
+    // the next spawn (e.g. Cursor's ReloadClient) can rebind it without
+    // EADDRINUSE retries.
+    let shuttingDown = false;
+    const shutdown = (reason) => {
+        if (shuttingDown)
+            return;
+        shuttingDown = true;
+        logToStderr(`[codetree] Shutting down (${reason})...`);
+        try {
+            watcher?.stop();
+        }
+        catch { /* ignore */ }
+        try {
+            ipc.stop();
+        }
+        catch { /* ignore */ }
+        try {
+            db.close();
+        }
+        catch { /* ignore */ }
         process.exit(0);
     };
-    process.on("SIGINT", shutdown);
-    process.on("SIGTERM", shutdown);
-    process.on("SIGHUP", shutdown);
+    process.on("SIGINT", () => shutdown("SIGINT"));
+    process.on("SIGTERM", () => shutdown("SIGTERM"));
+    process.on("SIGHUP", () => shutdown("SIGHUP"));
+    // The MCP host (Cursor / Claude Code / Antigravity) typically tears the
+    // server down by closing its stdio transport rather than sending SIGTERM
+    // — and SIGTERM doesn't reliably reach Node child processes on Windows
+    // anyway. Treat stdio close / stdin EOF as an authoritative shutdown
+    // signal so we don't keep the IPC port hostage.
+    transport.onclose = () => shutdown("transport closed");
+    process.stdin.on("end", () => shutdown("stdin end"));
+    process.stdin.on("close", () => shutdown("stdin close"));
 }
 /**
  * Log to stderr so it doesn't interfere with MCP stdio protocol on stdout.

package/dist/server/mcp-server.js.map

@@ -1 +1 @@
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+{"version":3,"file":"mcp-server.js","sourceRoot":"","sources":["../../src/server/mcp-server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,2CAA2C,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EACL,qBAAqB,EACrB,sBAAsB,GACvB,MAAM,oCAAoC,CAAC;AAC5C,OAAO,EAAE,UAAU,EAAuB,MAAM,cAAc,CAAC;AAC/D,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAChD,OAAO,EAAE,WAAW,EAAE,MAAM,uBAAuB,CAAC;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,UAAU,CAAC;AACrC,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC1D,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,WAAW,CAAC;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AAEzC,MAAM,SAAS,GAAG,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;AAE1D,SAAS,iBAAiB;IACxB,IAAI,CAAC;QACH,kDAAkD;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,cAAc,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC;QAC3F,OAAO,GAAG,CAAC,OAAO,IAAI,OAAO,CAAC;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,OAAO,CAAC;IACjB,CAAC;AACH,CAAC;AAED,KAAK,UAAU,IAAI;IACjB,cAAc;IACd,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,OAAO,CAAC,GAAG,EAAE,CAAC;IACvE,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,CAAC,CAAC;IAEvC,wBAAwB;IACxB,MAAM,EAAE,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC;IAChC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC;IAEhB,MAAM,KAAK,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC;IAC3D,MAAM,OAAO,GAAG,IAAI,OAAO,CAAC,MAAM,EAAE,EAAE,EAAE,KAAK,CAAC,CAAC;IAC/C,MAAM,OAAO,CAAC,IAAI,EAAE,CAAC;IAErB,mFAAmF;IACnF,MAAM,GAAG,GAAG,IAAI,SAAS,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IAC/C,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,KAAK,EAAE,CAAC;IAElC,yEAAyE;IACzE,0EAA0E;IAC1E,yEAAyE;IACzE,2CAA2C;IAC3C,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;QAChB,WAAW,CAAC,6EAA6E,CAAC,CAAC;QAC3F,EAAE,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,OAAO,GAAG,GAAG,CAAC,OAAO,EAAE,CAAC;IAC9B,WAAW,CAAC,iCAAiC,OAAO,KAAK,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC;IAE1F,qEAAqE;IACrE,wEAAwE;IACxE,yDAAyD;IACzD,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,IAAI,WAAW,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAClE,IAAI,OAAO,IAAI,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC;QACpC,OAAO,CAAC,KAAK,EAAE,CAAC;QAChB,WAAW,CAAC,iCAAiC,CAAC,CAAC;IACjD,CAAC;IAED,IAAI,OAAO,EAAE,CAAC;QACZ,WAAW,CAAC,2CAA2C,CAAC,CAAC;QACzD,OAAO,CAAC,QAAQ,CAAC;YACf,UAAU,EAAE,CAAC,OAAO,EAAE,KAAK,EAAE,EAAE;gBAC7B,IAAI,OAAO,GAAG,GAAG,KAAK,CAAC,EAAE,CAAC;oBACxB,WAAW,CAAC,sBAAsB,OAAO,IAAI,KAAK,WAAW,CAAC,CAAC;gBACjE,CAAC;YACH,CAAC;YACD,OAAO,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;gBACrB,WAAW,CAAC,6BAA6B,IAAI,KAAK,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;YACnE,CAAC;YACD,UAAU,EAAE,CAAC,KAAK,EAAE,EAAE;gBACpB,WAAW,CACT,8BAA8B,KAAK,CAAC,YAAY,IAAI,KAAK,CAAC,UAAU,UAAU;oBAC9E,GAAG,KAAK,CAAC,WAAW,aAAa,KAAK,CAAC,WAAW,IAAI,CACvD,CAAC;YACJ,CAAC;SACF,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE;YACf,WAAW,CAAC,iCAAiC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;QAC9D,CAAC,CAAC,CAAC;IACL,CAAC;SAAM,CAAC;QACN,WAAW,CAAC,8EAA8E,CAAC,CAAC;IAC9F,CAAC;IAED,2BAA2B;IAC3B,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IACrD,MAAM,UAAU,GAAG,gBAAgB,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IACzD,MAAM,aAAa,GAAG,mBAAmB,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACtD,MAAM,YAAY,GAAG,kBAAkB,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IAC7D,MAAM,WAAW,GAAG,iBAAiB,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAClD,MAAM,UAAU,GAAG,gBAAgB,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAChD,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IACrD,MAAM,SAAS,GAAG,eAAe,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IACvD,MAAM,WAAW,GAAG,iBAAiB,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAClD,MAAM,SAAS,GAAG,eAAe,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;IAEvD,MAAM,KAAK,GAAG,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,EAAE,YAAY,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,SAAS,CAAC,CAAC;IACxI,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IAEvD,oBAAoB;IACpB,MAAM,MAAM,GAAG,IAAI,MAAM,CACvB;QACE,IAAI,EAAE,UAAU;QAChB,OAAO,EAAE,iBAAiB,EAAE;KAC7B,EACD;QACE,YAAY,EAAE;YACZ,KAAK,EAAE,EAAE;SACV;KACF,CACF,CAAC;IAEF,aAAa;IACb,MAAM,CAAC,iBAAiB,CAAC,sBAAsB,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QAC5D,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACvB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,WAAW,EAAE,CAAC,CAAC,WAAW;YAC1B,WAAW,EAAE,CAAC,CAAC,WAAW;SAC3B,CAAC,CAAC;KACJ,CAAC,CAAC,CAAC;IAEJ,oBAAoB;IACpB,MAAM,CAAC,iBAAiB,CAAC,qBAAqB,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE;QAChE,MAAM,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC;QACjD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAE/B,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAO;gBACL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package/dist/server/tools/codetree-probe.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"codetree-probe.d.ts","sourceRoot":"","sources":["../../../src/server/tools/codetree-probe.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACtD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAE1D,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,KAAK,CAAC;QAAE,SAAS,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC,CAAC;IAC3D,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE,OAAO,CAAC;CACpB;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAiB3D,WAAW,KAAG,OAAO,CAAC,WAAW,CAAC;EAuD7D"}
+{"version":3,"file":"codetree-probe.d.ts","sourceRoot":"","sources":["../../../src/server/tools/codetree-probe.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACtD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAE1D,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,KAAK,CAAC;QAAE,SAAS,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC,CAAC;IAC3D,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE,OAAO,CAAC;CACpB;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAiB3D,WAAW,KAAG,OAAO,CAAC,WAAW,CAAC;EAmF7D"}

package/dist/server/tools/codetree-probe.js

@@ -22,31 +22,60 @@ export function createProbeTool(_config, indexer, db) {
             const limit = params.limit ?? 30;
             const q = params.query;
             const qLower = q.toLowerCase();
-            // Candidate file set
+            // Candidate file set.
+            //
+            // We deliberately apply file_pattern BEFORE any bounded fallback cap.
+            // The DB returns paths sorted alphabetically; on a 2k+ file repo the
+            // first MAX_FALLBACK_FILES files might all live under directories that
+            // don't match file_pattern at all, which used to silently return zero
+            // hits for queries whose answer lived past the cap. Filtering first
+            // means the bounded scan is over the *relevant* subset, not the
+            // alphabetically-earliest one.
             const MAX_FALLBACK_FILES = 500;
+            const patternFilter = params.file_pattern ? params.file_pattern.toLowerCase() : null;
             let candidatePaths;
             if (params.files && params.files.length > 0) {
                 candidatePaths = params.files;
+                if (patternFilter) {
+                    candidatePaths = candidatePaths.filter((fp) => fp.toLowerCase().includes(patternFilter));
+                }
             }
-            else if (q.length >= 3) {
-                const candidates = indexer.filesContainingAny([q]);
-                if (candidates.size === 0) {
-                    // Postings may be cold for non-identifier queries — fall back, but
-                    // bounded to avoid full-corpus scans.
-                    candidatePaths = db.getAllFiles().slice(0, MAX_FALLBACK_FILES).map((f) => f.path);
+            else {
+                // Build the pool of paths permitted by file_pattern (if any).
+                const allPaths = db.getAllFiles().map((f) => f.path);
+                const allowedByPattern = patternFilter
+                    ? allPaths.filter((fp) => fp.toLowerCase().includes(patternFilter))
+                    : allPaths;
+                // Try postings — works for both single-identifier queries ("Razorpay")
+                // AND multi-word queries ("fast-growing startups") because we tokenize
+                // the query into the same subtoken shape the indexer stores.
+                let postings = null;
+                if (q.length >= 3)
+                    postings = indexer.filesContainingQuery(q);
+                if (postings && postings.size > 0) {
+                    if (patternFilter) {
+                        const allowedSet = new Set(allowedByPattern);
+                        const intersected = [];
+                        for (const f of postings)
+                            if (allowedSet.has(f))
+                                intersected.push(f);
+                        candidatePaths = intersected.length > 0
+                            ? intersected
+                            // Postings hit but nothing matches the pattern. Don't claim the
+                            // string isn't there — fall back to a bounded scan over the
+                            // pattern subset so we still verify it directly.
+                            : allowedByPattern.slice(0, MAX_FALLBACK_FILES);
+                    }
+                    else {
+                        candidatePaths = Array.from(postings);
+                    }
                 }
                 else {
-                    candidatePaths = Array.from(candidates);
+                    // Postings cold (short query, non-identifier query, or genuinely
+                    // absent). Fall back to a bounded scan of the pattern-filtered pool.
+                    candidatePaths = allowedByPattern.slice(0, MAX_FALLBACK_FILES);
                 }
             }
-            else {
-                // Too short for postings — bounded scan only.
-                candidatePaths = db.getAllFiles().slice(0, MAX_FALLBACK_FILES).map((f) => f.path);
-            }
-            if (params.file_pattern) {
-                const p = params.file_pattern.toLowerCase();
-                candidatePaths = candidatePaths.filter((fp) => fp.toLowerCase().includes(p));
-            }
             const hits = [];
             let filesScanned = 0;
             let truncated = false;

package/dist/server/tools/codetree-probe.js.map

@@ -1 +1 @@
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+{"version":3,"file":"codetree-probe.js","sourceRoot":"","sources":["../../../src/server/tools/codetree-probe.ts"],"names":[],"mappings":"AAkBA;;;GAGG;AACH,MAAM,UAAU,eAAe,CAAC,OAAuB,EAAE,OAAgB,EAAE,EAAY;IACrF,OAAO;QACL,IAAI,EAAE,gBAAgB;QACtB,WAAW,EACT,wFAAwF;YACxF,0FAA0F;YAC1F,kEAAkE;QACpE,WAAW,EAAE;YACX,IAAI,EAAE,QAAiB;YACvB,UAAU,EAAE;gBACV,KAAK,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,sDAAsD,EAAE;gBAC9F,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,WAAW,EAAE,yCAAyC,EAAE;gBAC3G,YAAY,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,2CAA2C,EAAE;gBAC1F,KAAK,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,EAAE,qCAAqC,EAAE;aAC9E;YACD,QAAQ,EAAE,CAAC,OAAO,CAAC;SACpB;QACD,OAAO,EAAE,KAAK,EAAE,MAAmB,EAAwB,EAAE;YAC3D,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,IAAI,EAAE,CAAC;YACjC,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC;YACvB,MAAM,MAAM,GAAG,CAAC,CAAC,WAAW,EAAE,CAAC;YAE/B,sBAAsB;YACtB,EAAE;YACF,sEAAsE;YACtE,qEAAqE;YACrE,uEAAuE;YACvE,sEAAsE;YACtE,oEAAoE;YACpE,gEAAgE;YAChE,+BAA+B;YAC/B,MAAM,kBAAkB,GAAG,GAAG,CAAC;YAC/B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;YAErF,IAAI,cAAwB,CAAC;YAC7B,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5C,cAAc,GAAG,MAAM,CAAC,KAAK,CAAC;gBAC9B,IAAI,aAAa,EAAE,CAAC;oBAClB,cAAc,GAAG,cAAc,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC;gBAC3F,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,8DAA8D;gBAC9D,MAAM,QAAQ,GAAG,EAAE,CAAC,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;gBACrD,MAAM,gBAAgB,GAAG,aAAa;oBACpC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC;oBACnE,CAAC,CAAC,QAAQ,CAAC;gBAEb,uEAAuE;gBACvE,uEAAuE;gBACvE,6DAA6D;gBAC7D,IAAI,QAAQ,GAAuB,IAAI,CAAC;gBACxC,IAAI,CAAC,CAAC,MAAM,IAAI,CAAC;oBAAE,QAAQ,GAAG,OAAO,CAAC,oBAAoB,CAAC,CAAC,CAAC,CAAC;gBAE9D,IAAI,QAAQ,IAAI,QAAQ,CAAC,IAAI,GAAG,CAAC,EAAE,CAAC;oBAClC,IAAI,aAAa,EAAE,CAAC;wBAClB,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,gBAAgB,CAAC,CAAC;wBAC7C,MAAM,WAAW,GAAa,EAAE,CAAC;wBACjC,KAAK,MAAM,CAAC,IAAI,QAAQ;4BAAE,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC;gCAAE,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;wBACrE,cAAc,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC;4BACrC,CAAC,CAAC,WAAW;4BACb,gEAAgE;4BAChE,4DAA4D;4BAC5D,iDAAiD;4BACjD,CAAC,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAC;oBACpD,CAAC;yBAAM,CAAC;wBACN,cAAc,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;oBACxC,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,iEAAiE;oBACjE,qEAAqE;oBACrE,cAAc,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAC;gBACjE,CAAC;YACH,CAAC;YAED,MAAM,IAAI,GAAwB,EAAE,CAAC;YACrC,IAAI,YAAY,GAAG,CAAC,CAAC;YACrB,IAAI,SAAS,GAAG,KAAK,CAAC;YAEtB,KAAK,MAAM,EAAE,IAAI,cAAc,EAAE,CAAC;gBAChC,IAAI,IAAI,CAAC,MAAM,IAAI,KAAK,EAAE,CAAC;oBAAC,SAAS,GAAG,IAAI,CAAC;oBAAC,MAAM;gBAAC,CAAC;gBACtD,YAAY,EAAE,CAAC;gBACf,MAAM,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC;gBACvC,IAAI,CAAC,OAAO;oBAAE,SAAS;gBACvB,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC;oBAAE,SAAS;gBACtD,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;gBAClC,MAAM,WAAW,GAAa,EAAE,CAAC;gBACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBACtC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;wBAC5C,WAAW,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;wBACxB,IAAI,WAAW,CAAC,MAAM,IAAI,EAAE;4BAAE,MAAM,CAAC,eAAe;oBACtD,CAAC;gBACH,CAAC;gBACD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBAC3B,IAAI,CAAC,IAAI,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,YAAY,EAAE,WAAW,EAAE,CAAC,CAAC;gBAC1D,CAAC;YACH,CAAC;YAED,OAAO,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,SAAS,EAAE,CAAC;QACrD,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/server/tools/codetree-search.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"codetree-search.d.ts","sourceRoot":"","sources":["../../../src/server/tools/codetree-search.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACtD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAG1D,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,YAAY;IAC3B,OAAO,EAAE,KAAK,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,SAAS,EAAE,MAAM,CAAC;QAClB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,QAAQ,EAAE,OAAO,CAAC;KACnB,CAAC,CAAC;IACH,eAAe,CAAC,EAAE,KAAK,CAAC;QACtB,SAAS,EAAE,MAAM,CAAC;QAClB,WAAW,EAAE,MAAM,CAAC;QACpB,YAAY,EAAE,MAAM,CAAC;KACtB,CAAC,CAAC;IACH,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAsB3D,YAAY,KAAG,OAAO,CAAC,YAAY,CAAC;EA8G/D"}
+{"version":3,"file":"codetree-search.d.ts","sourceRoot":"","sources":["../../../src/server/tools/codetree-search.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACtD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAG1D,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,YAAY;IAC3B,OAAO,EAAE,KAAK,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,SAAS,EAAE,MAAM,CAAC;QAClB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,QAAQ,EAAE,OAAO,CAAC;KACnB,CAAC,CAAC;IACH,eAAe,CAAC,EAAE,KAAK,CAAC;QACtB,SAAS,EAAE,MAAM,CAAC;QAClB,WAAW,EAAE,MAAM,CAAC;QACpB,YAAY,EAAE,MAAM,CAAC;KACtB,CAAC,CAAC;IACH,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAsB3D,YAAY,KAAG,OAAO,CAAC,YAAY,CAAC;EAyI/D"}

package/dist/server/tools/codetree-search.js

@@ -73,34 +73,57 @@ export function createSearchTool(config, indexer, db) {
                 const queryLower = params.query.toLowerCase();
                 // Non-global regex — simpler semantics, no lastIndex foot-gun.
                 const regex = new RegExp(escapeRegex(params.query), "i");
-                // Pick candidate set:
-                //   ≥3 chars  → trigram index → token postings → all files (last resort)
-                //   <3 chars  → too short to index meaningfully, but we cap the corpus
-                //               at MAX_FALLBACK_FILES to avoid full-repo scans.
+                // Pick candidate set.
+                //
+                // Apply file_pattern BEFORE any fallback cap. The DB returns paths in
+                // alphabetical order, so on a 2k+ file repo the bounded-fallback used
+                // to silently miss anything past the first MAX_FALLBACK_FILES — even
+                // when file_pattern explicitly named a folder that lived past the cap.
+                //
+                //   ≥3 chars  → trigram index → token postings (tokenized) → bounded
+                //               scan of pattern-filtered files (last resort)
+                //   <3 chars  → bounded scan of pattern-filtered files
                 const MAX_FALLBACK_FILES = 500;
+                const patternFilter = params.file_pattern ? params.file_pattern.toLowerCase() : null;
+                const allPaths = db.getAllFiles().map((f) => f.path);
+                const allowedByPattern = patternFilter
+                    ? allPaths.filter((fp) => fp.toLowerCase().includes(patternFilter))
+                    : allPaths;
                 let candidatePaths;
                 if (params.query.length >= 3) {
+                    const narrowFromIndex = (raw) => {
+                        if (!patternFilter)
+                            return raw;
+                        const allowedSet = new Set(allowedByPattern);
+                        return raw.filter((fp) => allowedSet.has(fp));
+                    };
                     const trigramCandidates = db.searchByTrigrams(params.query, limit * 5);
-                    if (trigramCandidates.length > 0) {
-                        candidatePaths = trigramCandidates;
+                    let narrowed = narrowFromIndex(trigramCandidates);
+                    if (narrowed.length > 0) {
+                        candidatePaths = narrowed;
                     }
                     else {
-                        const postings = indexer.filesContainingAny([params.query]);
-                        if (postings.size > 0) {
-                            candidatePaths = Array.from(postings);
+                        const postings = indexer.filesContainingQuery(params.query);
+                        const postingArr = postings ? Array.from(postings) : [];
+                        narrowed = narrowFromIndex(postingArr);
+                        if (narrowed.length > 0) {
+                            candidatePaths = narrowed;
                         }
                         else {
-                            candidatePaths = db.getAllFiles().map((f) => f.path);
+                            // Index couldn't narrow — bounded scan over the pattern subset.
+                            candidatePaths = allowedByPattern.slice(0, Math.max(MAX_FALLBACK_FILES, allowedByPattern.length <= MAX_FALLBACK_FILES ? allowedByPattern.length : MAX_FALLBACK_FILES));
                         }
                     }
                 }
                 else {
-                    // Short query: bounded scan — agents shouldn't pay full-corpus cost
-                    // for 1- or 2-char queries (they're almost never useful anyway).
-                    candidatePaths = db.getAllFiles().slice(0, MAX_FALLBACK_FILES).map((f) => f.path);
+                    // Short query: bounded scan over pattern subset.
+                    candidatePaths = allowedByPattern.slice(0, MAX_FALLBACK_FILES);
                 }
                 for (const filePath of candidatePaths) {
-                    if (params.file_pattern && !filePath.toLowerCase().includes(params.file_pattern.toLowerCase()))
+                    // Pattern check is now redundant for index-derived candidates, but
+                    // kept as a safety net for caller-supplied trigram results that
+                    // somehow leak past the narrowFromIndex filter (e.g. stale rows).
+                    if (patternFilter && !filePath.toLowerCase().includes(patternFilter))
                         continue;
                     const content = indexer.readCached(filePath);
                     if (!content)

package/dist/server/tools/codetree-search.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "codetree-claude",
-  "version": "1.5.3",
+  "version": "1.5.6",
   "description": "MCP server & CLI: codebase index + cache for Claude Code, Cursor, OpenAI Codex, Google Antigravity/Gemini. Model Context Protocol tools (codetree_read, codetree_search, …), hooks on Claude, rules on other IDEs. Token savings, SQLite index, symbol search, session memory.",
   "type": "module",
   "main": "dist/index.js",