codesift-mcp 0.15.5 → 0.19.2

package/dist/cli/auto-prune.d.ts

@@ -0,0 +1,16 @@
+export declare function pruneIsDue(dataDir: string, now: number, intervalMs?: number): Promise<boolean>;
+export declare function recordPruneRun(dataDir: string, now: number): Promise<void>;
+export interface AutoPruneOptions {
+    dataDir: string;
+    cliEntry: string;
+    env?: NodeJS.ProcessEnv;
+    now?: () => number;
+    /** Injected in tests; production spawns a detached child. */
+    spawnChild?: (cliEntry: string) => void;
+}
+export declare function runAutoPruneOnce(options: AutoPruneOptions): Promise<"ran" | "throttled" | "disabled">;
+/** Schedule the sweep after the daemon is serving. Never awaited, never blocks a request. */
+export declare function scheduleAutoPrune(options: AutoPruneOptions & {
+    delayMs?: number;
+}): NodeJS.Timeout;
+//# sourceMappingURL=auto-prune.d.ts.map

package/dist/cli/auto-prune.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/auto-prune.js

@@ -0,0 +1,87 @@
+import { spawn } from "node:child_process";
+import { readFile, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+/**
+ * Retention for indexes whose repository is gone.
+ *
+ * Nothing was reclaiming them. `prune` exists, and it is a command a person has to type — no timer,
+ * no cron, nothing in the daemon called it. Measured 2026-09-02: 267 orphaned registry entries had
+ * accumulated holding **58.7 GB**, and the data directory had gone 65 GB → 98 GB in sixteen days,
+ * about 2 GB a day. Every worktree gets its own index by design (answering from a sibling's tree is
+ * the H19 failure this prevents), so a workflow that creates ten worktrees at a time and deletes
+ * them leaves ten indexes behind each round.
+ *
+ * Run in a DETACHED CHILD, never in-process. `handlePrune` reaches `die()` on each of its safety
+ * guards — unreadable registry, zero repos, every entry stale — and `die` ends the process. In the
+ * daemon that would turn a refused prune into a dead server for every client on the machine.
+ *
+ * The child is also why this needs no LaunchAgent: the maintenance lives in the product, is
+ * versioned with it and is covered by its tests, rather than in a plist nobody edits again.
+ */
+const PRUNE_INTERVAL_MS = 24 * 60 * 60 * 1000;
+/** Long enough that the first clients are served before any maintenance competes with them. */
+const PRUNE_START_DELAY_MS = 5 * 60 * 1000;
+function stampPath(dataDir) {
+    return join(dataDir, "last-prune.json");
+}
+export async function pruneIsDue(dataDir, now, intervalMs = PRUNE_INTERVAL_MS) {
+    try {
+        const raw = await readFile(stampPath(dataDir), "utf-8");
+        const at = JSON.parse(raw).at;
+        if (typeof at !== "number" || !Number.isFinite(at))
+            return true;
+        // A stamp in the FUTURE means a clock change, not a prune five hours from now. Treating it as
+        // "not due" would park retention until the clock caught up, which on a laptop can be never.
+        if (at > now)
+            return true;
+        return now - at >= intervalMs;
+    }
+    catch {
+        // No stamp yet, or unreadable — due. Erring towards running is right: the failure this exists
+        // to prevent is 58 GB of dead indexes, and prune's own guards refuse anything ambiguous.
+        return true;
+    }
+}
+export async function recordPruneRun(dataDir, now) {
+    try {
+        await writeFile(stampPath(dataDir), JSON.stringify({ at: now }), "utf-8");
+    }
+    catch {
+        // A stamp that cannot be written means the next start prunes again. Wasteful, not harmful —
+        // and far better than failing a daemon start over a maintenance bookkeeping file.
+    }
+}
+export async function runAutoPruneOnce(options) {
+    const env = options.env ?? process.env;
+    if (env["CODESIFT_AUTO_PRUNE"] === "0" || env["CODESIFT_AUTO_PRUNE"] === "false") {
+        return "disabled";
+    }
+    const now = (options.now ?? Date.now)();
+    if (!(await pruneIsDue(options.dataDir, now)))
+        return "throttled";
+    // Stamp BEFORE spawning. A prune that crashes must not re-run on every restart of a
+    // crash-looping daemon — that is how a maintenance task becomes the outage.
+    await recordPruneRun(options.dataDir, now);
+    if (options.spawnChild) {
+        options.spawnChild(options.cliEntry);
+        return "ran";
+    }
+    const child = spawn(process.execPath, [options.cliEntry, "prune", "--json"], {
+        detached: true,
+        stdio: "ignore",
+    });
+    child.unref();
+    return "ran";
+}
+/** Schedule the sweep after the daemon is serving. Never awaited, never blocks a request. */
+export function scheduleAutoPrune(options) {
+    const timer = setTimeout(() => {
+        void runAutoPruneOnce(options).catch(() => {
+            // Maintenance is best-effort by construction: the next start tries again.
+        });
+    }, options.delayMs ?? PRUNE_START_DELAY_MS);
+    // Must not hold the process open — a daemon told to exit should exit.
+    timer.unref();
+    return timer;
+}
+//# sourceMappingURL=auto-prune.js.map

package/dist/cli/auto-prune.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands-admin.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands-admin.js

@@ -81,8 +81,19 @@ async function handleSetup(args, flags) {
     const rawScheme = getFlag(flags, "scheme");
     const daemonScheme = rawScheme === "https" ? "https" : rawScheme === "http" ? "http" : undefined;
     const insecureTransport = getBoolFlag(flags, "insecure-transport") ?? false;
+    // --project writes the client config into THIS project instead of the user's home, and pins this
+    // directory into the URL. It exists because a client whose MCP config is global cannot use the
+    // shared daemon at all: one URL carries one directory, so one global entry cannot describe two
+    // projects, and the client falls back to a stdio process per session.
+    //
+    // Without --project, `--http` writes the GLOBAL entry as a bare daemon URL (no ?cwd=), which is
+    // the transport half; each project's own config then supplies the directory half by overriding
+    // the same key. A global entry that pinned one directory would be actively wrong for every other
+    // project on the machine.
+    const projectScope = getBoolFlag(flags, "project") ?? false;
     const options = {
         hooks, rules, force, gitHooks, http,
+        ...(projectScope ? { projectScope: true, cwd: process.cwd() } : http ? { cwd: null } : {}),
         ...(port !== undefined ? { port } : {}),
         ...(daemonHost ? { host: daemonHost } : {}),
         ...(daemonToken ? { token: daemonToken } : {}),

package/dist/cli/commands-admin.js.map

@@ -1 +1 @@
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package/dist/cli/commands-daemon.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"commands-daemon.d.ts","sourceRoot":"","sources":["../../src/cli/commands-daemon.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AACvC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAC;AAMrD,mEAAmE;AACnE,eAAO,MAAM,mBAAmB,OAAO,CAAC;AAExC,MAAM,MAAM,YAAY,GAAG,gBAAgB,CAAC;AAE5C,uEAAuE;AACvE,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAEtF;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAQnD;AAED,mEAAmE;AACnE,wBAAgB,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAUpF;AAqCD;;;;;;;;GAQG;AACH,wBAAsB,WAAW,CAC/B,IAAI,GAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAO,GAC5E,OAAO,CAAC,YAAY,CAAC,CAkEvB;AAED;;GAEG;AACH,iBAAe,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CA0BvE;AAED,OAAO,EAAE,WAAW,EAAE,CAAC"}

package/dist/cli/commands-daemon.js

@@ -1,6 +1,9 @@
 import { join } from "node:path";
 import { readFileSync, writeFileSync, mkdirSync, unlinkSync } from "node:fs";
 import { getFlag, getNumFlag, output, die } from "./args.js";
+import { scheduleAutoPrune } from "./auto-prune.js";
+import { loadConfig } from "../config.js";
+import { fileURLToPath } from "node:url";
 /** Default daemon port — clients point here via `setup --http`. */
 export const DEFAULT_DAEMON_PORT = 7077;
 /** Lockfile paths for the daemon in a given data dir (~/.codesift). */
@@ -46,6 +49,32 @@ function readDaemonPid(pidPath) {
         return null;
     }
 }
+/**
+ * Timestamped startup trace on stderr, one line per stage.
+ *
+ * The daemon used to print NOTHING between launch and its first served request, and a start that
+ * takes minutes is indistinguishable from one that will never finish: measured 2026-09-24, a fresh
+ * `launchctl load` left the process alive with **no listening socket for 9+ minutes** while the box
+ * sat at load 155, and the only way to learn where it was came from `sample <pid>` reading V8
+ * frames. A hang now names its stage by being the line that never arrives after the last one
+ * printed — which is also why the stages are logged on ENTRY-to-next rather than as one summary at
+ * the end. Default on: nobody sets a debug flag before the outage they did not expect.
+ *
+ * Elapsed is measured from PROCESS START (`process.uptime()`), not from entry to this function. Most
+ * of that 9-minute start was spent before `startDaemon` was even called — `sample` caught the main
+ * thread inside ESM module evaluation — so a clock that starts here would have reported a healthy
+ * few hundred milliseconds and hidden the entire delay. The first line's own number is therefore the
+ * measurement that matters: it is the cost of importing the CLI.
+ *
+ * Off with `CODESIFT_DAEMON_BOOT_TRACE=0`.
+ */
+function bootTracer() {
+    return (stage) => {
+        if (process.env["CODESIFT_DAEMON_BOOT_TRACE"] === "0")
+            return;
+        console.error(`[codesift] boot +${Math.round(process.uptime() * 1000)}ms ${stage}`);
+    };
+}
 /**
  * Acquire the daemon lock and start the shared HTTP server.
  *
@@ -56,15 +85,18 @@ function readDaemonPid(pidPath) {
  * `close()` removes the lockfiles, so a graceful SIGTERM leaves a clean slate.
  */
 export async function startDaemon(opts = {}) {
+    const trace = bootTracer();
     const { loadConfig } = await import("../config.js");
     const dataDir = opts.dataDir ?? loadConfig().dataDir;
     const { pidPath, portPath } = daemonLockPaths(dataDir);
+    trace("config");
     mkdirSync(dataDir, { recursive: true });
     const { DatabaseSync } = await import("node:sqlite");
     const lockDb = new DatabaseSync(join(dataDir, "daemon-lock.db"));
     try {
         lockDb.exec("PRAGMA busy_timeout = 0; CREATE TABLE IF NOT EXISTS daemon_lock (id INTEGER PRIMARY KEY);");
         lockDb.exec("BEGIN EXCLUSIVE");
+        trace("lock acquired");
     }
     catch (error) {
         try {
@@ -105,6 +137,8 @@ export async function startDaemon(opts = {}) {
         }
         catch { /* stale or absent */ }
         const { startHttpServer } = await import("../server.js");
+        // The heavy one: this pulls the whole tool surface, every parser and the storage layer.
+        trace("server module imported");
         const httpOpts = {};
         if (opts.port !== undefined)
             httpOpts.port = opts.port;
@@ -113,6 +147,7 @@ export async function startDaemon(opts = {}) {
         if (opts.token !== undefined)
             httpOpts.token = opts.token;
         handle = await startHttpServer(httpOpts);
+        trace(`listening on ${handle.port}`);
         writeFileSync(portPath, String(handle.port));
         const origClose = handle.close;
         return {
@@ -153,6 +188,12 @@ async function handleServe(_args, flags) {
         return;
     }
     output({ status: "serving", url: handle.url, port: handle.port, pid: process.pid }, flags);
+    // Reclaim indexes whose repository is gone. Only the daemon does this — it is the one
+    // long-lived process per machine, so a stdio server per session would run it N times over.
+    scheduleAutoPrune({
+        dataDir: loadConfig().dataDir,
+        cliEntry: fileURLToPath(new URL("../cli.js", import.meta.url)),
+    });
     const shutdown = () => {
         void handle.close().then(() => process.exit(0));
     };

package/dist/cli/commands-daemon.js.map

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package/dist/cli/commands-index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"commands-index.d.ts","sourceRoot":"","sources":["../../src/cli/commands-index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AAGvC,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,MAAM,EAAE,MAAM,GACb;IAAE,SAAS,EAAE,OAAO,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAMtC;AA6DD,iBAAe,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CA+CtE;AAED,iBAAe,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAuB1E;AAED,iBAAe,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAIvE;AAED,iBAAe,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAK3E;AAED,iBAAe,wBAAwB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAQnF;AAED,OAAO,EAAE,WAAW,EAAE,eAAe,EAAE,WAAW,EAAE,gBAAgB,EAAE,wBAAwB,EAAE,CAAC"}

package/dist/cli/commands-index.js

@@ -61,6 +61,14 @@ async function runEmbeddingChild(repoName, rootPath) {
 }
 async function handleIndex(args, flags) {
     const path = requireArg(args, 0, "path");
+    // `embed-child` has guarded itself against a dead parent for a while; THIS process, the one that
+    // spawns it, did not. Measured 2026-08-29: an agent's shell died, this command was reparented to
+    // launchd and kept running, so the child's ppid check saw a live parent and never fired — the
+    // pair burned 813% CPU and 4.9 GB for 1 h 10 min on a worktree that had already been deleted.
+    // Guarding the parent is what makes the child's guard reachable.
+    const { exitWhenOrphaned, exitWhenRootGone } = await import("./orphan-guard.js");
+    exitWhenOrphaned();
+    exitWhenRootGone(path);
     const { indexFolder } = await import("../tools/index-tools.js");
     // Keep onnxruntime out of THIS process; the embedding runs in a child below.
     process.env["CODESIFT_EMBED_OUT_OF_PROCESS"] = "1";

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@@ -1 +1 @@
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+{"version":3,"file":"commands-index.js","sourceRoot":"","sources":["../../src/cli/commands-index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,mBAAmB,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAE1F,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAa,EACb,MAAc;IAEd,MAAM,QAAQ,GAAG,IAAI,GAAG,KAAK,CAAC;IAC9B,OAAO;QACL,SAAS,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC;QACpC,IAAI,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE;KACpE,CAAC;AACJ,CAAC;AAED,8EAA8E;AAC9E,iBAAiB;AACjB,8EAA8E;AAE9E;;;;;;;;;;;GAWG;AACH,KAAK,UAAU,iBAAiB,CAAC,QAAgB,EAAE,QAAgB;IACjE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,2BAA2B,CAAC,CAAC;IACnE,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,MAAM,CAAC,cAAc,CAAC,CAAC;IACpD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,CAAC;IACrD,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,MAAM,CAAC,UAAU,CAAC,CAAC;IACnD,MAAM,EAAE,OAAO,EAAE,IAAI,EAAE,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,CAAC;IAEpD,MAAM,MAAM,GAAG,UAAU,EAAE,CAAC;IAC5B,IAAI,CAAC,MAAM,CAAC,iBAAiB;QAAE,OAAO,CAAC,+BAA+B;IAEtE,MAAM,SAAS,GAAG,YAAY,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,gBAAgB,CAAC,CAAC;IACpF,MAAM,EAAE,qBAAqB,EAAE,GAAG,MAAM,MAAM,CAAC,yBAAyB,CAAC,CAAC;IAE1E,MAAM,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,EAAE;QAClC,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC,WAAW,EAAE,SAAS,EAAE,QAAQ,EAAE,QAAQ,CAAC,EAAE;YAClF,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,SAAS,CAAC;YACpC,GAAG,EAAE,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,6BAA6B,EAAE,GAAG,EAAE;SAC5D,CAAC,CAAC;QAEH,IAAI,SAAS,GAAG,KAAK,CAAC;QACtB,IAAI,UAAU,GAAG,EAAE,CAAC;QACpB,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,GAAW,EAAE,EAAE;YACtC,MAAM,IAAI,GAAG,mBAAmB,CAAC,UAAU,EAAE,GAAG,CAAC,QAAQ,EAAE,EAAE,qBAAqB,CAAC,CAAC;YACpF,IAAI,IAAI,CAAC,SAAS;gBAAE,SAAS,GAAG,IAAI,CAAC;YACrC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC;QACzB,CAAC,CAAC,CAAC;QACH,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE;YACxB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,iCAAiC,GAAG,CAAC,OAAO,IAAI,CAAC,CAAC;YACvE,OAAO,EAAE,CAAC;QACZ,CAAC,CAAC,CAAC;QACH,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,+CAA+C,IAAI,IAAI,MAAM,MAAM;oBACjE,4CAA4C,CAC/C,CAAC;YACJ,CAAC;YACD,OAAO,EAAE,CAAC;QACZ,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC;AAED,KAAK,UAAU,WAAW,CAAC,IAAc,EAAE,KAAY;IACrD,MAAM,IAAI,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC,EAAE,MAAM,CAAC,CAAC;IAEzC,iGAAiG;IACjG,iGAAiG;IACjG,8FAA8F;IAC9F,8FAA8F;IAC9F,iEAAiE;IACjE,MAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,GAAG,MAAM,MAAM,CAAC,mBAAmB,CAAC,CAAC;IACjF,gBAAgB,EAAE,CAAC;IACnB,gBAAgB,CAAC,IAAI,CAAC,CAAC;IAEvB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,yBAAyB,CAAC,CAAC;IAEhE,6EAA6E;IAC7E,OAAO,CAAC,GAAG,CAAC,+BAA+B,CAAC,GAAG,GAAG,CAAC;IAEnD,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,IAAI,EAAE;QACrC,WAAW,EAAE,WAAW,CAAC,KAAK,EAAE,aAAa,CAAC;QAC9C,aAAa,EAAE,mBAAmB,CAAC,KAAK,EAAE,eAAe,CAAC;QAC1D,KAAK,EAAE,WAAW,CAAC,KAAK,EAAE,UAAU,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS;KACnE,CAAC,CAAC;IAEH,4EAA4E;IAC5E,2EAA2E;IAC3E,0BAA0B;IAC1B,MAAM,EAAE,sBAAsB,EAAE,GAAG,MAAM,MAAM,CAAC,wCAAwC,CAAC,CAAC;IAC1F,MAAM,sBAAsB,EAAE,CAAC;IAE/B,MAAM,IAAI,GAAI,MAAmC,EAAE,IAAI,CAAC;IACxD,MAAM,IAAI,GAAI,MAAmC,EAAE,IAAI,CAAC;IACxD,IAAI,IAAI,IAAI,IAAI;QAAE,MAAM,iBAAiB,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IAEtD,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEtB,2EAA2E;IAC3E,6EAA6E;IAC7E,6EAA6E;IAC7E,8EAA8E;IAC9E,8EAA8E;IAC9E,6EAA6E;IAC7E,IAAI,WAAW,CAAC,KAAK,EAAE,UAAU,CAAC,KAAK,IAAI,EAAE,CAAC;QAC5C,OAAO,CAAC,KAAK,CACX,uBAAuB,IAAI,IAAI,IAAI,iCAAiC;cAClE,2DAA2D,CAC9D,CAAC;IACJ,CAAC;AACH,CAAC;AAED,KAAK,UAAU,eAAe,CAAC,IAAc,EAAE,KAAY;IACzD,MAAM,GAAG,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;IACvC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,MAAM,CAAC,yBAAyB,CAAC,CAAC;IAE9D,6EAA6E;IAC7E,4EAA4E;IAC5E,4EAA4E;IAC5E,qEAAqE;IACrE,OAAO,CAAC,GAAG,CAAC,+BAA+B,CAAC,GAAG,GAAG,CAAC;IAEnD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,EAAE;QAClC,MAAM,EAAE,OAAO,CAAC,KAAK,EAAE,QAAQ,CAAC;QAChC,aAAa,EAAE,mBAAmB,CAAC,KAAK,EAAE,eAAe,CAAC;KAC3D,CAAC,CAAC;IAEH,MAAM,EAAE,sBAAsB,EAAE,GAAG,MAAM,MAAM,CAAC,wCAAwC,CAAC,CAAC;IAC1F,MAAM,sBAAsB,EAAE,CAAC;IAE/B,MAAM,IAAI,GAAI,MAAmC,EAAE,IAAI,CAAC;IACxD,MAAM,IAAI,GAAI,MAAmC,EAAE,IAAI,CAAC;IACxD,IAAI,IAAI,IAAI,IAAI;QAAE,MAAM,iBAAiB,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IAEtD,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;AACxB,CAAC;AAED,KAAK,UAAU,WAAW,CAAC,KAAe,EAAE,KAAY;IACtD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,yBAAyB,CAAC,CAAC;IACjE,MAAM,MAAM,GAAG,MAAM,YAAY,EAAE,CAAC;IACpC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;AACxB,CAAC;AAED,KAAK,UAAU,gBAAgB,CAAC,IAAc,EAAE,KAAY;IAC1D,MAAM,IAAI,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC,EAAE,MAAM,CAAC,CAAC;IACzC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,MAAM,CAAC,yBAAyB,CAAC,CAAC;IACpE,MAAM,MAAM,GAAG,MAAM,eAAe,CAAC,IAAI,CAAC,CAAC;IAC3C,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,EAAE,IAAI,EAAE,EAAE,KAAK,CAAC,CAAC;AAC/C,CAAC;AAED,KAAK,UAAU,wBAAwB,CAAC,IAAc,EAAE,KAAY;IAClE,MAAM,WAAW,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;IAC5B,MAAM,EAAE,kBAAkB,EAAE,GAAG,MAAM,MAAM,CAAC,gCAAgC,CAAC,CAAC;IAE9E,MAAM,MAAM,GAAG,MAAM,kBAAkB,CAAC,WAAW,CAAC,CAAC;IACrD,I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package/dist/cli/commands-maintenance.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"commands-maintenance.d.ts","sourceRoot":"","sources":["../../src/cli/commands-maintenance.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AAGvC;;;;;;GAMG;AACH,iBAAe,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAKvE;AAiWD,iBAAe,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CA+ClF;AAED,OAAO,EAAE,WAAW,EAAE,sBAAsB,EAAE,CAAC"}
+{"version":3,"file":"commands-maintenance.d.ts","sourceRoot":"","sources":["../../src/cli/commands-maintenance.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AAGvC;;;;;;GAMG;AACH,iBAAe,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAKvE;AA2eD,iBAAe,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CA+ClF;AAED,OAAO,EAAE,WAAW,EAAE,sBAAsB,EAAE,CAAC"}

package/dist/cli/commands-maintenance.js

@@ -14,7 +14,7 @@ async function handlePrune(_args, flags) {
     await withRegistryLock(registryPath, () => handlePruneLocked(flags, registryPath));
 }
 async function handlePruneLocked(flags, registryPath) {
-    const { readFileSync, readdirSync, statSync, unlinkSync } = await import("node:fs");
+    const { readFileSync, readdirSync, statSync, unlinkSync, existsSync } = await import("node:fs");
     const { join } = await import("node:path");
     const { loadConfig } = await import("../config.js");
     const dataDir = loadConfig().dataDir;
@@ -235,17 +235,49 @@ async function handlePruneLocked(flags, registryPath) {
             return true;
         }
     };
+    // An abandoned half of an interrupted write is garbage no matter WHOSE it is.
+    //
+    // `artifactPattern()` learned the `.tmp.*` / `.generation.*` tails so these could be reclaimed —
+    // and then the live-hash check below made that unreachable for any repo still on disk, which is
+    // essentially all of them (measured 2026-09-27: 1,507 of 1,511 registry roots present). So the
+    // tails were collected only for repos that were *also* being de-registered. Result on this
+    // machine: 149 temp files holding 11.15 GB, the oldest from 31 July, surviving a `prune` that had
+    // run the day before and reported success.
+    //
+    // A temp file is never live data by construction: readers open the target name, never the tail.
+    // The rules that decide are therefore the same two the in-process sweeper uses — an hour of age,
+    // and a writer that is no longer running — not registry membership.
+    const tempTail = /\.(?:tmp|generation)\./;
+    const orphanTempAgeMs = 60 * 60 * 1000;
+    const { writerPidIsAlive, PID_TRUST_WINDOW_MS: pidTrustWindowMs } = await import("../storage/_shared.js");
     let files = 0, bytes = 0, kept = 0;
     for (const name of readdirSync(dataDir)) {
         const m = re.exec(name);
         if (!m)
             continue;
+        const isTempTail = tempTail.test(name);
         // A stale entry removed during THIS run gets one full run of retention.
         // The next prune re-evaluates its database metadata before collecting it.
-        if (live.has(m[1]) || staleHashes.has(m[1])) {
+        if (!isTempTail && (live.has(m[1]) || staleHashes.has(m[1]))) {
             kept++;
             continue;
         }
+        // Pid liveness is trusted only inside the sweeper's own window — see PID_TRUST_WINDOW_MS. A
+        // recycled pid must not pin an abandoned write forever; that is the leak, not the guard.
+        if (isTempTail) {
+            let mtimeMs = 0;
+            try {
+                mtimeMs = statSync(join(dataDir, name)).mtimeMs;
+            }
+            catch {
+                kept++;
+                continue;
+            }
+            if (Date.now() - mtimeMs < pidTrustWindowMs && writerPidIsAlive(name)) {
+                kept++;
+                continue;
+            }
+        }
         const full = join(dataDir, name);
         try {
             const fileStat = statSync(full);
@@ -253,7 +285,16 @@ async function handlePruneLocked(flags, registryPath) {
             // committed its registry entry. Delay collection for one run and also
             // re-read registry immediately before every destructive unlink.
             const ageMs = Date.now() - fileStat.mtimeMs;
-            if (ageMs < pruneGraceMs || registryProtectsHash(m[1])) {
+            // A temp tail gets the sweeper's hour rather than the 5-minute grace, and is NOT protected by
+            // its hash being registered — that protection is the whole reason these accumulated. The hour
+            // is what covers a write still in flight whose pid we could not read from the name.
+            if (isTempTail) {
+                if (ageMs < orphanTempAgeMs) {
+                    kept++;
+                    continue;
+                }
+            }
+            else if (ageMs < pruneGraceMs || registryProtectsHash(m[1])) {
                 kept++;
                 continue;
             }
@@ -264,6 +305,74 @@ async function handlePruneLocked(flags, registryPath) {
         }
         catch { /* skip unreadable/already-gone */ }
     }
+    // Reclaim BM25 caches written by a format this build cannot read.
+    //
+    // These DO carry a repo hash, so the sweep above sees them — and skips them, because the hash is
+    // live. That is correct for a readable cache and wrong for one no build can read: a format bump
+    // makes every existing file garbage, and it is only overwritten when that repo is indexed again,
+    // which for a repo nobody touches is never. Measured at the v1 -> v2 bump: 47.78 GB on this machine.
+    //
+    // Judged by the file's OWN header, not by its age or its hash — that is the only thing that says
+    // which format it is. An unreadable or headerless first line is left alone: the file is then either
+    // mid-write or something this code does not understand, and neither is a reason to delete.
+    let bm25Superseded = 0;
+    if (!dryRun) {
+        const { bm25FormatVersion } = await import("../search/bm25-store.js");
+        const current = bm25FormatVersion();
+        const { open } = await import("node:fs/promises");
+        for (const name of readdirSync(dataDir)) {
+            if (!/^[0-9a-f]{8,}\.bm25\.ndjson$/.test(name))
+                continue;
+            const full = join(dataDir, name);
+            let version;
+            // Capture the identity the version decision is made ABOUT. Every writer here is
+            // temp-then-rename, so between reading this header and unlinking the file another process can
+            // atomically put a CURRENT-format index in its place — and the unlink would then delete a valid
+            // cache and force an expensive rebuild. Compared again immediately before the unlink below.
+            let seenMtimeMs;
+            let seenIno;
+            try {
+                const seen = statSync(full);
+                seenMtimeMs = seen.mtimeMs;
+                seenIno = seen.ino;
+            }
+            catch {
+                continue;
+            }
+            try {
+                const handle = await open(full, "r");
+                try {
+                    // The header is the first line; 64 KiB is far more than it can be.
+                    const buf = Buffer.allocUnsafe(64 * 1024);
+                    const { bytesRead } = await handle.read(buf, 0, buf.length, 0);
+                    const firstLine = buf.subarray(0, bytesRead).toString("utf-8").split("\n", 1)[0] ?? "";
+                    version = JSON.parse(firstLine).v;
+                }
+                finally {
+                    await handle.close();
+                }
+            }
+            catch {
+                continue;
+            }
+            if (typeof version !== "number" || version >= current)
+                continue;
+            try {
+                const fileStat = statSync(full);
+                if (Date.now() - fileStat.mtimeMs < pruneGraceMs)
+                    continue;
+                // Same file, unchanged since its header was read? A different inode or mtime means a writer
+                // replaced it, and what sits there now is not what the version check looked at.
+                if (fileStat.mtimeMs !== seenMtimeMs || fileStat.ino !== seenIno)
+                    continue;
+                unlinkSync(full);
+                bytes += fileStat.size;
+                files++;
+                bm25Superseded++;
+            }
+            catch { /* already gone */ }
+        }
+    }
     // Shared-cache versions have no repository hash prefix, so the artifact
     // sweep cannot discover superseded formats. Keep the current version and
     // reclaim only older derived cache files.
@@ -288,7 +397,68 @@ async function handlePruneLocked(flags, registryPath) {
         }
         catch { /* skip unreadable/already-gone */ }
     }
+    // Checkpoint write-ahead logs that no longer have a writer.
+    //
+    // SQLite truncates a `-wal` when the LAST connection closes cleanly. This server's connections
+    // frequently do not: a stdio server exits on client disconnect, the daemon has OOM'd, and a
+    // `launchctl unload` is a signal. Each of those leaves the log on disk, and nothing ever comes
+    // back to that database to fold it in — so it is derived data with no owner, which is exactly what
+    // this command is for. Measured 2026-09-27: 1,488 logs holding 4.17 GB, of which 682 were above
+    // 64 KB; checkpointing those brought the total to 0.01 GB.
+    //
+    // A live index is the normal case here, not an edge case, so this must never disturb one: opening
+    // a database that another process holds throws or the checkpoint is refused, and either way the
+    // log is left exactly as it was. Small logs are skipped rather than opened — a busy index will
+    // just rewrite its own, and the bytes are not worth the syscalls.
+    let walBefore = 0, walAfter = 0, walCheckpointed = 0;
+    if (!dryRun) {
+        const { DatabaseSync } = await import("node:sqlite");
+        for (const name of readdirSync(dataDir)) {
+            if (!name.endsWith(".index.db-wal"))
+                continue;
+            const full = join(dataDir, name);
+            let size;
+            try {
+                size = statSync(full).size;
+            }
+            catch {
+                continue;
+            }
+            walBefore += size;
+            if (size < 64 * 1024) {
+                walAfter += size;
+                continue;
+            }
+            const dbPath = join(dataDir, name.slice(0, -"-wal".length));
+            // `new DatabaseSync(path)` CREATES the file when it is absent, so a stray `-wal` with no
+            // database — what a partial delete or an earlier prune leaves — would have this command
+            // manufacture an empty database and then "checkpoint" it. Reclaiming bytes must not create
+            // artifacts. Raised by the cross-model review of this release.
+            if (!existsSync(dbPath)) {
+                walAfter += size;
+                continue;
+            }
+            try {
+                const db = new DatabaseSync(dbPath);
+                try {
+                    db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
+                    walCheckpointed++;
+                }
+                finally {
+                    db.close();
+                }
+            }
+            catch { /* held open elsewhere, or unreadable — leave the log alone */ }
+            try {
+                walAfter += statSync(full).size;
+            }
+            catch { /* gone */ }
+        }
+    }
     output({
+        bm25_superseded_format: bm25Superseded,
+        wal_checkpointed: walCheckpointed,
+        wal_reclaimed_gb: +((walBefore - walAfter) / 1e9).toFixed(2),
         indeterminate_databases: indeterminate.length,
         indeterminate_examples: indeterminate.slice(0, 5),
         rescued_repos: rescued.length,