codesift-mcp 0.15.5 → 0.19.2

package/dist/server.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 import { McpServer } from "@modelcontextprotocol/server";
-import { StdioServerTransport } from "@modelcontextprotocol/server/stdio";
+import { StdioServerTransport, serveStdio } from "@modelcontextprotocol/server/stdio";
 import { millisSinceLastActivity, releaseCachedIndexes } from "./tools/index-tools/state.js";
 import { loadConfig } from "./config.js";
 import { registerTools, enableFrameworkToolBundle, frontLoadHiddenToolsForFrozenHost, shouldFrontLoadHiddenTools, } from "./register-tools.js";
@@ -13,11 +13,15 @@ import { setupHooksForPlatform } from "./cli/setup.js";
 import { detectPlatform, detectPlatformFromClientInfo } from "./cli/platform.js";
 import { createRequire } from "node:module";
 import { timingSafeEqual } from "node:crypto";
-import { resolve as pathResolve } from "node:path";
+import { resolve as pathResolve, isAbsolute, join } from "node:path";
+import { homedir } from "node:os";
 import { statSync } from "node:fs";
+import { readVitals, classifyVitals, startVitals } from "./server-helpers/health-vitals.js";
 import { fileURLToPath } from "node:url";
 import { isLoopbackHost } from "./utils/loopback.js";
 import { runWithRequestContext } from "./server-helpers/request-context.js";
+import { envelopeClientName, observeInbound } from "./server-helpers/stdio-envelope.js";
+import { enableShownSourceLedger } from "./server-helpers/shown-source.js";
 // Re-export for test compatibility
 export { buildResponseHint, resetSessionState } from "./server-helpers.js";
 export { resetSession } from "./storage/session-state.js";
@@ -149,8 +153,65 @@ function codeReplacedUnderUs() {
  * nothing. Not a security boundary (the daemon is loopback-only and already
  * serves every indexed repo to any local caller) but it keeps a typo from
  * silently resolving every repo to garbage.
+ *
+ * Two shapes come from VS Code-derived clients writing `?cwd=${workspaceFolder}`,
+ * which is what lets ONE GLOBAL entry serve every project on a client that has no
+ * per-project MCP config. Both were measured against Cursor 1.0 (probe, 2026-08-27):
+ *
+ *   - `~/DEV/thing` — Cursor expands the variable to a TILDE path, not an absolute
+ *     one. `pathResolve` expands `~` against the process cwd, which for a
+ *     launchd-started daemon is `/`, producing `/~/DEV/thing`; that fails `statSync`
+ *     and the directory silently vanished. Expanding it here is what makes the
+ *     single-entry configuration work at all.
+ *   - `${workspaceFolder}` verbatim — a window with NO folder open leaves the
+ *     placeholder unexpanded. It must not become a directory name.
+ *
+ * A rejected value is announced once. The whole reason this cost a full
+ * investigation is that an unusable cwd degraded into "no cwd" without a word,
+ * and the symptom surfaced far away as `Repository "local/" not found`.
  */
-function cwdFromUrl(rawUrl) {
+const warnedCwdValues = new Set();
+const MAX_WARNED_CWD_VALUES = 32;
+function warnUnusableCwd(value, why) {
+    // Bounded: the value comes from a URL, so an unbounded set is a memory leak a
+    // client could drive. Past the cap we stay quiet rather than grow.
+    if (warnedCwdValues.has(value) || warnedCwdValues.size >= MAX_WARNED_CWD_VALUES)
+        return;
+    warnedCwdValues.add(value);
+    console.error(`[codesift] ignoring ?cwd=${value} — ${why}. Repo auto-resolution will fail for this ` +
+        `client; pass an absolute path, or an explicit repo argument.`);
+}
+/** Expand a leading `~`. `~user` is left alone — it cannot be resolved reliably. */
+function expandTilde(value) {
+    if (value === "~")
+        return homedir();
+    if (value.startsWith("~/"))
+        return join(homedir(), value.slice(2));
+    return value;
+}
+/**
+ * Which client this connection belongs to, from `?client=` in the URL.
+ *
+ * Written by `codesift setup <platform> --http`. It travels in the URL for the same reason `cwd`
+ * does: stateless serving has no session, and the `initialized` notification arrives on an instance
+ * that never handled `initialize`, so its clientInfo is empty — measured, not assumed.
+ */
+export function clientFromUrl(rawUrl) {
+    const q = rawUrl.indexOf("?");
+    if (q < 0)
+        return undefined;
+    try {
+        const value = new URLSearchParams(rawUrl.slice(q + 1)).get("client");
+        // Bounded and alphanumeric: this selects a code path, so it is not a place for free text.
+        if (!value || !/^[a-z][a-z0-9-]{0,31}$/i.test(value))
+            return undefined;
+        return value.toLowerCase();
+    }
+    catch {
+        return undefined;
+    }
+}
+export function cwdFromUrl(rawUrl) {
     const q = rawUrl.indexOf("?");
     if (q < 0)
         return undefined;
@@ -163,11 +224,27 @@ function cwdFromUrl(rawUrl) {
     }
     if (!value)
         return undefined;
+    // An unexpanded client-side placeholder, not a path.
+    if (value.includes("${")) {
+        warnUnusableCwd(value, "the client did not expand this variable (window with no folder open?)");
+        return undefined;
+    }
+    const expanded = expandTilde(value);
+    if (!isAbsolute(expanded)) {
+        // Resolving a relative path against the daemon's cwd (`/` under launchd) is
+        // meaningless and would silently name the wrong directory.
+        warnUnusableCwd(value, "not an absolute path");
+        return undefined;
+    }
     try {
-        const resolved = pathResolve(value);
-        return statSync(resolved).isDirectory() ? resolved : undefined;
+        const resolved = pathResolve(expanded);
+        if (statSync(resolved).isDirectory())
+            return resolved;
+        warnUnusableCwd(value, "not a directory");
+        return undefined;
     }
     catch {
+        warnUnusableCwd(value, "no such directory");
         return undefined;
     }
 }
@@ -267,7 +344,37 @@ export async function startHttpServer(opts = {}) {
      * makes more than one process — or a remote host — possible at all without a
      * shared session store.
      */
-    const handler = createMcpHandler(() => createCodesiftServer(), { legacy: "stateless" });
+    const envPlatformForHttp = detectPlatform();
+    /** Set by the HTTP handler just before delegating, read by the server factory. */
+    let clientForNextServer;
+    /**
+     * One daemon, clients that want different lists.
+     *
+     * Codex freezes its tool list at session start, so a tool not offered up front is unreachable for
+     * the whole session — measured 2026-08-29, a Codex client on the daemon saw 90 tools where the
+     * same build over stdio gives it 181, and `find_dead_code` did not exist as far as it was
+     * concerned. Claude Code is the opposite: it refreshes on demand and STOPS USING CodeSift when
+     * handed everything (3e1ec6c, adoption down >90%).
+     *
+     * So the decision is made per REQUEST, from `?client=`, and the front-load is deliberately not
+     * remembered at process scope — otherwise one Codex session would hand every Claude Code session
+     * the full list too.
+     */
+    const handler = createMcpHandler(() => {
+        const s = createCodesiftServer();
+        // NOT from the async context: the handler builds this server outside the request's
+        // AsyncLocalStorage scope — measured, `currentClient()` is undefined here even when the URL
+        // carried one. The value is stashed by the HTTP handler immediately before it delegates, on the
+        // same tick, which is the only moment both are in scope.
+        const client = clientForNextServer;
+        const platform = envPlatformForHttp !== "unknown"
+            ? envPlatformForHttp
+            : detectPlatformFromClientInfo(client ?? "");
+        if (client && shouldFrontLoadHiddenTools(platform)) {
+            frontLoadHiddenToolsForFrozenHost({ remember: false });
+        }
+        return s;
+    }, { legacy: "stateless" });
     const nodeHandler = toNodeHandler(handler);
     let inFlight = 0;
     const httpServer = http.createServer((req, res) => {
@@ -279,6 +386,16 @@ export async function startHttpServer(opts = {}) {
                     // code, and this state means "every tool call from here will fail" — reporting it inside
                     // a 200 body is how the previous version managed to look healthy while serving nothing.
                     const stale = codeReplacedUnderUs();
+                    // Who holds the heap, not just how much of it. `?caches=0` opts out for a probe that only
+                    // wants liveness; the report walks the cached indexes to price them, which is cheap but not
+                    // free on a process holding several hundred thousand symbols.
+                    const { readCacheReport } = await import("./server-helpers/cache-report.js");
+                    // A parsed query parameter, not a substring match: `?notcaches=0` and `?x=caches=0y` both
+                    // satisfied `includes` and silently turned the report off. Harmless here — it gates an
+                    // optional diagnostic on a loopback endpoint — but a flag that can be set by accident is a
+                    // flag nobody can reason about. Raised as a NIT by the CQ audit of this release.
+                    const wantsCaches = new URL(url, "http://127.0.0.1").searchParams.get("caches") !== "0";
+                    const caches = wantsCaches ? await readCacheReport() : undefined;
                     res.writeHead(stale ? 503 : 200, { "content-type": "application/json" });
                     res.end(JSON.stringify(stale
                         ? {
@@ -288,7 +405,21 @@ export async function startHttpServer(opts = {}) {
                             reason: "the files this daemon started from were replaced (rebuild); lazily imported modules will fail until it restarts",
                             remedy: "launchctl kickstart -k gui/$(id -u)/com.codesift.daemon",
                         }
-                        : { status: "ok", sessions: inFlight, version: PKG_VERSION }));
+                        : (() => {
+                            // Liveness was never the question — the daemon was alive through all three
+                            // incidents. `busy` keeps the 200 on purpose: slow is not down, and a session
+                            // told "down" stops using tools it could still have used.
+                            const vitals = readVitals();
+                            const { status, reasons } = classifyVitals(vitals);
+                            return {
+                                status,
+                                sessions: inFlight,
+                                version: PKG_VERSION,
+                                vitals,
+                                ...(caches ? { caches } : {}),
+                                ...(reasons.length > 0 ? { reasons } : {}),
+                            };
+                        })()));
                     return;
                 }
                 if (token) {
@@ -302,6 +433,9 @@ export async function startHttpServer(opts = {}) {
                 // The caller's directory, pinned per request. Statelessness makes this
                 // the natural carrier: there is no session to have learned it once.
                 const cwd = cwdFromUrl(url);
+                // Stashed for the server factory, which runs outside this request's async context —
+                // measured: currentClient() is undefined there even when the URL carried one.
+                clientForNextServer = clientFromUrl(url);
                 inFlight++;
                 try {
                     await (cwd
@@ -325,6 +459,7 @@ export async function startHttpServer(opts = {}) {
             }
         })();
     });
+    startVitals();
     await new Promise((resolve) => httpServer.listen(opts.port ?? 0, host, resolve));
     const addr = httpServer.address();
     const port = typeof addr === "object" && addr ? addr.port : (opts.port ?? 0);
@@ -365,42 +500,16 @@ async function autoEnableFrameworkToolsFromPackageJson(cwd) {
         // Non-fatal — this is a startup optimization
     }
 }
-async function main() {
-    const startTs = Date.now();
-    // Shared HTTP daemon mode: one process serves all editor windows, embeddings
-    // load once. `codesift serve` (Task 7) sets CODESIFT_TRANSPORT=http.
-    if (process.env["CODESIFT_TRANSPORT"] === "http") {
-        const port = Number(process.env["CODESIFT_HTTP_PORT"]) || 7077;
-        const handle = await startHttpServer({ port });
-        console.error(`CodeSift MCP HTTP server on ${handle.url}`);
-        autoEnableFrameworkToolsFromPackageJson(process.cwd()).catch(() => { });
-        autoIndexCurrentRepo(process.cwd()).catch((err) => {
-            console.error("[codesift] auto-index failed:", err);
-        });
-        autoDiscoverConversations(process.cwd()).catch((err) => {
-            console.error("[codesift] conversation auto-discovery failed:", err);
-        });
-        return;
-    }
-    // stdio only: stdin EOF/close is the canonical "parent died" signal. Attached
-    // here (not globally) so the HTTP daemon path is unaffected.
-    process.stdin.on("end", () => shutdownOnParentGone("stdin end"));
-    process.stdin.on("close", () => shutdownOnParentGone("stdin close"));
-    startIdleCacheRelease();
-    const transport = new StdioServerTransport();
-    // Diagnostic transport hooks. Primary fix for "-32000: Connection closed" is
-    // event-loop yielding inside heavy tools (perf-tools, hotspot-tools, project-tools);
-    // these handlers leave a stderr trace if any residual transport drop occurs.
-    transport.onclose = () => {
-        console.error(`[codesift] transport closed at uptime=${Date.now() - startTs}ms`);
-        // The client disconnected — do NOT keep running as an orphan. Background
-        // timers (watcher/auto-index) would otherwise hold the event loop open and
-        // the process would linger under launchd forever. See shutdownOnParentGone.
-        shutdownOnParentGone("transport close");
-    };
-    transport.onerror = (err) => {
-        console.error(`[codesift] transport error at uptime=${Date.now() - startTs}ms:`, err.message);
-    };
+/**
+ * Per-connection client handling for stdio: hook auto-install and the frozen-list front-load.
+ *
+ * `onClientIdentified` runs once, as soon as the client has named itself — in the `initialized`
+ * notification on a 2025-era connection, or on the first enveloped message of a 2026-07-28 one
+ * (which has no handshake; see stdio-envelope.ts). Either way it lands before the host's first
+ * tools/list is answered, which is the only window where enabling a tool still reaches a host
+ * that freezes its list.
+ */
+function createStdioClientHooks() {
     const envPlatform = detectPlatform();
     let hooksInstalledFor = null;
     const installHooks = (platform, reason) => {
@@ -411,14 +520,15 @@ async function main() {
             console.error(`[codesift] hook auto-install failed (${reason}:${platform}):`, err);
         });
     };
-    server.server.oninitialized = () => {
-        const clientName = server.server.getClientVersion()?.name ?? "";
+    let clientIdentified = false;
+    const onClientIdentified = (clientName) => {
+        if (clientIdentified)
+            return;
+        clientIdentified = true;
         const clientPlatform = detectPlatformFromClientInfo(clientName);
         const platform = envPlatform !== "unknown" ? envPlatform : clientPlatform;
         // Front-load reveal-dependent tools for hosts that freeze their tool list
-        // at session start. This runs in the `initialized` notification, i.e. before
-        // the client's first tools/list, which is the only window where enabling a
-        // tool still reaches that host. See FROZEN_LIST_FALLBACK_TOOL_NAMES.
+        // at session start. See FROZEN_LIST_FALLBACK_TOOL_NAMES.
         if (shouldFrontLoadHiddenTools(platform)) {
             const enabled = frontLoadHiddenToolsForFrozenHost();
             if (enabled.length > 0) {
@@ -430,7 +540,81 @@ async function main() {
             return;
         installHooks(clientPlatform === "unknown" ? "claude" : clientPlatform, clientName || "fallback");
     };
-    await server.connect(transport);
+    return { envPlatform, installHooks, onClientIdentified };
+}
+/**
+ * Serve MCP over stdio through `serveStdio`, not `server.connect`: it owns the era decision. A bare
+ * connect() serves only the 2025-era handshake — a 2026-07-28 client's `server/discover` came back
+ * `Method not found`, so the client never received the server instructions either.
+ *
+ * The factory may run twice (a modern probe instance discarded in favour of a legacy one); the
+ * first call reuses the module-level server so the common path is unchanged, later calls build a
+ * fresh one. Front-loaded tools are remembered at process scope, so a fresh instance picks them up
+ * in registerTools.
+ */
+function startStdioTransport(startTs, onClientIdentified) {
+    const wire = observeInbound(new StdioServerTransport(), (message) => {
+        const name = envelopeClientName(message);
+        if (name !== undefined)
+            onClientIdentified(name);
+    }, () => {
+        console.error(`[codesift] transport closed at uptime=${Date.now() - startTs}ms`);
+        // The client disconnected — do NOT keep running as an orphan. Background
+        // timers (watcher/auto-index) would otherwise hold the event loop open and
+        // the process would linger under launchd forever. See shutdownOnParentGone.
+        shutdownOnParentGone("transport close");
+    }, {
+        // serveStdio swallows a failed transport start and returns no promise to await, so without
+        // this the process would log "started" and serve nothing. `await server.connect()` used to
+        // reach main()'s fatal-exit path; this restores that contract.
+        onStartFailed: (err) => {
+            console.error("Fatal error starting CodeSift MCP server:", err);
+            process.exit(1);
+        },
+    });
+    let usedModuleServer = false;
+    serveStdio(() => {
+        const instance = usedModuleServer ? createCodesiftServer() : server;
+        usedModuleServer = true;
+        instance.server.oninitialized = () => {
+            onClientIdentified(instance.server.getClientVersion()?.name ?? "");
+        };
+        return instance;
+    }, {
+        transport: wire,
+        // Diagnostic trace. Primary fix for "-32000: Connection closed" is event-loop yielding inside
+        // heavy tools; this leaves a stderr line if any residual transport fault occurs.
+        onerror: (err) => {
+            console.error(`[codesift] transport error at uptime=${Date.now() - startTs}ms:`, err.message);
+        },
+    });
+}
+async function main() {
+    const startTs = Date.now();
+    // Shared HTTP daemon mode: one process serves all editor windows, embeddings
+    // load once. `codesift serve` (Task 7) sets CODESIFT_TRANSPORT=http.
+    if (process.env["CODESIFT_TRANSPORT"] === "http") {
+        const port = Number(process.env["CODESIFT_HTTP_PORT"]) || 7077;
+        const handle = await startHttpServer({ port });
+        console.error(`CodeSift MCP HTTP server on ${handle.url}`);
+        autoEnableFrameworkToolsFromPackageJson(process.cwd()).catch(() => { });
+        autoIndexCurrentRepo(process.cwd()).catch((err) => {
+            console.error("[codesift] auto-index failed:", err);
+        });
+        autoDiscoverConversations(process.cwd()).catch((err) => {
+            console.error("[codesift] conversation auto-discovery failed:", err);
+        });
+        return;
+    }
+    // stdio only: stdin EOF/close is the canonical "parent died" signal. Attached
+    // here (not globally) so the HTTP daemon path is unaffected.
+    process.stdin.on("end", () => shutdownOnParentGone("stdin end"));
+    process.stdin.on("close", () => shutdownOnParentGone("stdin close"));
+    startIdleCacheRelease();
+    // Over stdio the process is one conversation, so "already shown" means shown to THIS agent.
+    enableShownSourceLedger();
+    const client = createStdioClientHooks();
+    startStdioTransport(startTs, client.onClientIdentified);
     console.error("CodeSift MCP server started");
     // Telemetry: one-time consent notice (stderr) + background flush timer.
     // No-op when telemetry is off or no endpoint is configured (safe default).
@@ -447,8 +631,8 @@ async function main() {
         console.error("[codesift] conversation auto-discovery failed:", err);
     });
     // Auto-install hooks for the detected platform (idempotent)
-    if (envPlatform !== "unknown") {
-        installHooks(envPlatform, "env");
+    if (client.envPlatform !== "unknown") {
+        client.installHooks(client.envPlatform, "env");
     }
 }
 // Auto-run only when executed as the entrypoint (`node dist/server.js`), not when

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/storage/_shared.d.ts

@@ -13,6 +13,31 @@
  * never fail the write it is protecting.
  */
 export declare function cleanupOrphanTempFiles(targetPath: string, minAgeMs?: number): Promise<number>;
+/**
+ * How long a live pid in a temp name is trusted as an in-flight write.
+ *
+ * PIDS RECYCLE. macOS wraps them at 99,999 and this machine churns agent processes fast enough to
+ * get there in days, after which an unrelated live process pins a dead writer's temp file forever —
+ * the leak this function exists to close, reintroduced through its own safety guard. Past this
+ * window a matching pid is far more likely a reused number than a write still in flight: the largest
+ * artifact on this install is 1.7 GB, and nothing legitimate is still flushing after a day.
+ */
+export declare const PID_TRUST_WINDOW_MS: number;
+/**
+ * True when a `.generation.<pid>.<uuid>` or `.tmp.<pid>` name belongs to a process that still exists.
+ *
+ * `kill(pid, 0)` sends no signal; it only asks whether the id is addressable. EPERM means the
+ * process exists and belongs to someone else — still alive, so still hands off. Anything else, and
+ * any name without a parsable pid, is treated as dead: this runs beside an age guard, and the cost
+ * of being wrong in that direction is one orphan surviving another hour.
+ *
+ * The `.tmp.<pid>` arm is what makes it SAFE to sweep on behalf of the stream writers
+ * (`bm25-store`, `edge-cache`). Their temp file is the only shape here whose write can outlive the
+ * age guard: the largest bm25 artifact on this machine is 1.7 GB, and a daemon whose event loop is
+ * seconds late takes far longer than an hour to flush it. Without this, adding a sweep to those
+ * writers would turn a slow save into a deleted one.
+ */
+export declare function writerPidIsAlive(entry: string): boolean;
 /**
  * Write content to a file atomically using a write-rename strategy.
  * 1. Ensures the parent directory exists (mkdir -p).
@@ -44,7 +69,7 @@ export declare function atomicWriteBuffer(targetPath: string, buf: Buffer): Prom
  * sqlitePathFor, …) rather than written out independently, and asserted against them in
  * tests, so adding an artifact kind without teaching prune about it fails the build.
  */
-export declare const ARTIFACT_SUFFIXES: readonly ["index.json", "index.db", "index.db-wal", "index.db-shm", "embeddings.ndjson", "embeddings.meta.json", "chunks.ndjson", "chunk-embeddings.ndjson", "bm25.json", "graph.json", "snapshot.json"];
+export declare const ARTIFACT_SUFFIXES: readonly ["index.json", "index.db", "index.db-wal", "index.db-shm", "embeddings.ndjson", "embeddings.meta.json", "chunks.ndjson", "chunk-embeddings.ndjson", "bm25.json", "bm25.ndjson", "import-edges.ndjson", "graph.json", "snapshot.json"];
 /**
  * Matches `<hash>.<known artifact suffix>`, with an optional `.tmp.<ts>` tail so the
  * abandoned halves of an interrupted atomic write are reclaimed too. Capture group 1 is the

package/dist/storage/_shared.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"_shared.d.ts","sourceRoot":"","sources":["../../src/storage/_shared.ts"],"names":[],"mappings":"AAGA;;;;;;;;;;;;;GAaG;AACH,wBAAsB,sBAAsB,CAC1C,UAAU,EAAE,MAAM,EAClB,QAAQ,SAAiB,GACxB,OAAO,CAAC,MAAM,CAAC,CAkBjB;AAED;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,UAAU,EAAE,MAAM,EAClB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,IAAI,CAAC,CAgBf;AAED;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,UAAU,EAAE,MAAM,EAClB,GAAG,EAAE,MAAM,GACV,OAAO,CAAC,IAAI,CAAC,CAaf;AAED;;;;;;;;;;;;;GAaG;AACH,eAAO,MAAM,iBAAiB,YAC5B,YAAY,EACZ,UAAU,EACV,cAAc,EACd,cAAc,EACd,mBAAmB,EACnB,sBAAsB,EACtB,eAAe,EACf,yBAAyB,EACzB,WAAW,EACX,YAAY,EACZ,eAAe,CACP,CAAC;AAEX;;;;GAIG;AACH,wBAAgB,eAAe,IAAI,MAAM,CAGxC"}
+{"version":3,"file":"_shared.d.ts","sourceRoot":"","sources":["../../src/storage/_shared.ts"],"names":[],"mappings":"AAGA;;;;;;;;;;;;;GAaG;AACH,wBAAsB,sBAAsB,CAC1C,UAAU,EAAE,MAAM,EAClB,QAAQ,SAAiB,GACxB,OAAO,CAAC,MAAM,CAAC,CAmCjB;AAYD;;;;;;;;GAQG;AACH,eAAO,MAAM,mBAAmB,QAAsB,CAAC;AAEvD;;;;;;;;;;;;;GAaG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAWvD;AAED;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,UAAU,EAAE,MAAM,EAClB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,IAAI,CAAC,CAgBf;AAED;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,UAAU,EAAE,MAAM,EAClB,GAAG,EAAE,MAAM,GACV,OAAO,CAAC,IAAI,CAAC,CAaf;AAED;;;;;;;;;;;;;GAaG;AACH,eAAO,MAAM,iBAAiB,YAC5B,YAAY,EACZ,UAAU,EACV,cAAc,EACd,cAAc,EACd,mBAAmB,EACnB,sBAAsB,EACtB,eAAe,EACf,yBAAyB,EACzB,WAAW,EACX,aAAa,EACb,qBAAqB,EACrB,YAAY,EACZ,eAAe,CACP,CAAC;AAEX;;;;GAIG;AACH,wBAAgB,eAAe,IAAI,MAAM,CAQxC"}

package/dist/storage/_shared.js

@@ -16,18 +16,36 @@ import { basename, dirname, join } from "node:path";
  */
 export async function cleanupOrphanTempFiles(targetPath, minAgeMs = 60 * 60 * 1000) {
     const dir = dirname(targetPath);
-    const prefix = `${basename(targetPath)}.tmp.`;
+    const base = basename(targetPath);
+    // TWO shapes, not one. `atomicWriteFile` writes `<target>.tmp.<ts>`; `chunk-store` writes
+    // `<target>.generation.<pid>.<uuid>`. Only the first was ever swept, so the second accumulated
+    // untouched — measured 2026-09-05: 164 files, 19.6 GB, across 26 process ids of which 24 were
+    // long dead. They are invisible to `prune` too until the pattern above learns the tail.
+    const prefixes = [`${base}.tmp.`, `${base}.generation.`];
     let removed = 0;
     try {
         const cutoff = Date.now() - minAgeMs;
         for (const entry of await readdir(dir)) {
-            if (!entry.startsWith(prefix))
+            if (!prefixes.some((prefix) => entry.startsWith(prefix)))
                 continue;
+            // A generation file whose WRITER IS STILL RUNNING is an in-flight write, not an orphan. The
+            // age guard alone would eventually delete one: a large embedding batch can outlive the hour,
+            // and deleting it mid-write turns a slow save into a corrupt one.
+            //
+            // PIDS RECYCLE, so that protection has to expire. macOS wraps them at 99,999 and this machine
+            // churns agent processes fast enough to get there in days — after which an unrelated live
+            // process can pin a dead writer's temp file forever, which is the leak this function exists to
+            // close. Past `PID_TRUST_WINDOW_MS` a name that still matches something running is far more
+            // likely a reused number than a write that has been in flight for a day. The largest artifact
+            // on this install is 1.7 GB; nothing legitimate is still flushing after 24 hours.
             const full = join(dir, entry);
             try {
                 const info = await stat(full);
                 if (info.mtimeMs > cutoff)
                     continue;
+                const age = Date.now() - info.mtimeMs;
+                if (age < PID_TRUST_WINDOW_MS && writerPidIsAlive(entry))
+                    continue;
                 await unlink(full);
                 removed++;
             }
@@ -37,6 +55,54 @@ export async function cleanupOrphanTempFiles(targetPath, minAgeMs = 60 * 60 * 10
     catch { /* unreadable dir — nothing to clean */ }
     return removed;
 }
+/**
+ * Largest number in a temp name that can plausibly be a process id.
+ *
+ * `.tmp.<n>` is ambiguous: `bm25-store` and `edge-cache` put a PID there, `embedding-store` puts
+ * `Date.now()`. A timestamp read as a pid would be asked about — harmlessly, since `kill` answers
+ * ESRCH for it — but bounding the range says which shape is meant instead of relying on that
+ * accident. macOS caps pids at 99,999 and Linux's `pid_max` ceiling is 2^22.
+ */
+const MAX_PLAUSIBLE_PID = 4 * 1024 * 1024;
+/**
+ * How long a live pid in a temp name is trusted as an in-flight write.
+ *
+ * PIDS RECYCLE. macOS wraps them at 99,999 and this machine churns agent processes fast enough to
+ * get there in days, after which an unrelated live process pins a dead writer's temp file forever —
+ * the leak this function exists to close, reintroduced through its own safety guard. Past this
+ * window a matching pid is far more likely a reused number than a write still in flight: the largest
+ * artifact on this install is 1.7 GB, and nothing legitimate is still flushing after a day.
+ */
+export const PID_TRUST_WINDOW_MS = 24 * 60 * 60 * 1000;
+/**
+ * True when a `.generation.<pid>.<uuid>` or `.tmp.<pid>` name belongs to a process that still exists.
+ *
+ * `kill(pid, 0)` sends no signal; it only asks whether the id is addressable. EPERM means the
+ * process exists and belongs to someone else — still alive, so still hands off. Anything else, and
+ * any name without a parsable pid, is treated as dead: this runs beside an age guard, and the cost
+ * of being wrong in that direction is one orphan surviving another hour.
+ *
+ * The `.tmp.<pid>` arm is what makes it SAFE to sweep on behalf of the stream writers
+ * (`bm25-store`, `edge-cache`). Their temp file is the only shape here whose write can outlive the
+ * age guard: the largest bm25 artifact on this machine is 1.7 GB, and a daemon whose event loop is
+ * seconds late takes far longer than an hour to flush it. Without this, adding a sweep to those
+ * writers would turn a slow save into a deleted one.
+ */
+export function writerPidIsAlive(entry) {
+    const match = /\.(?:generation|tmp)\.(\d+)(?:\.|$)/.exec(entry);
+    if (!match)
+        return false;
+    const pid = Number(match[1]);
+    if (!Number.isInteger(pid) || pid <= 0 || pid > MAX_PLAUSIBLE_PID)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (err) {
+        return err.code === "EPERM";
+    }
+}
 /**
  * Write content to a file atomically using a write-rename strategy.
  * 1. Ensures the parent directory exists (mkdir -p).
@@ -111,6 +177,8 @@ export const ARTIFACT_SUFFIXES = [
     "chunks.ndjson",
     "chunk-embeddings.ndjson",
     "bm25.json",
+    "bm25.ndjson",
+    "import-edges.ndjson",
     "graph.json",
     "snapshot.json",
 ];
@@ -121,6 +189,9 @@ export const ARTIFACT_SUFFIXES = [
  */
 export function artifactPattern() {
     const suffixes = ARTIFACT_SUFFIXES.map((s) => s.replace(/[.\\+*?[^\]$(){}=!<>|:#-]/g, "\\$&"));
-    return new RegExp(`^([0-9a-f]{8,})\\.(?:${suffixes.join("|")})(?:\\.tmp\\..*)?$`);
+    // The abandoned-write tails are BOTH shapes. `.tmp.<ts>` comes from `atomicWriteFile`;
+    // `.generation.<pid>.<uuid>` comes from `chunk-store`, and prune could not see it — measured
+    // 2026-09-05, 164 such files holding 19.6 GB that neither cleanup path could reach.
+    return new RegExp(`^([0-9a-f]{8,})\\.(?:${suffixes.join("|")})(?:\\.tmp\\..*|\\.generation\\..*)?$`);
 }
 //# sourceMappingURL=_shared.js.map

package/dist/storage/_shared.js.map

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package/dist/storage/index-migration.d.ts.map

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