codesift-mcp 0.13.1 → 0.15.0

package/dist/storage/index-version.js

@@ -0,0 +1,87 @@
+import { classifyStorageError } from "./sqlite-index-store.js";
+/**
+ * Return every language whose stored extractor version differs from the bundled version.
+ * Newly added extractors are tolerated until the index actually contains that language.
+ */
+export function collectExtractorVersionMismatches(index, currentVersions) {
+    const stored = index.extractor_version ?? {};
+    const storedKeys = Object.keys(stored);
+    const indexedLanguages = new Set();
+    for (const file of index.files)
+        indexedLanguages.add(file.language);
+    const out = [];
+    if (index.files.length === 0 && storedKeys.length === 0) {
+        const langKeys = Object.keys(currentVersions);
+        if (langKeys.length === 0)
+            return [];
+        out.push({ language: "*", expected: "any", actual: "empty_index" });
+        return out;
+    }
+    for (const lang of Object.keys(currentVersions)) {
+        const expected = currentVersions[lang];
+        const actual = stored[lang];
+        if (expected === actual)
+            continue;
+        if (actual === undefined && !indexedLanguages.has(lang))
+            continue;
+        out.push({
+            language: lang,
+            expected: expected ?? "unknown",
+            actual: actual ?? "missing",
+        });
+    }
+    return out;
+}
+export function isExtractorVersionCurrent(index, currentVersions) {
+    if (!index.extractor_version)
+        return false;
+    return collectExtractorVersionMismatches(index, currentVersions).length === 0;
+}
+/**
+ * Load an index and turn extractor drift or storage failures into structured results.
+ * The facade injects its backend-agnostic reader to keep this module independent of it.
+ */
+export async function loadVersionAwareIndex(indexPath, currentVersions, readIndex) {
+    let parsed;
+    try {
+        parsed = await readIndex(indexPath);
+    }
+    catch (err) {
+        const code = classifyStorageError(err);
+        if (code === null)
+            throw err;
+        return {
+            status: "unreadable",
+            reason: "storage_error",
+            code,
+            message: err instanceof Error ? err.message : String(err),
+        };
+    }
+    try {
+        if (!parsed)
+            return null;
+        const mismatches = collectExtractorVersionMismatches(parsed, currentVersions);
+        if (mismatches.length > 0) {
+            const first = mismatches[0];
+            return {
+                status: "stale",
+                reason: "extractor_version_mismatch",
+                language: first.language,
+                expected_version: first.expected,
+                actual_version: first.actual,
+                ...(mismatches.length > 1
+                    ? {
+                        mismatch_detail: mismatches
+                            .map((m) => `${m.language}: expected ${m.expected}, got ${m.actual}`)
+                            .join("; "),
+                    }
+                    : {}),
+            };
+        }
+        return { status: "ok", index: parsed };
+    }
+    catch {
+        return null;
+    }
+}
+//# sourceMappingURL=index-version.js.map

package/dist/storage/index-version.js.map

@@ -0,0 +1 @@
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package/dist/storage/registry.d.ts

@@ -7,8 +7,16 @@ export declare function loadRegistry(registryPath: string): Promise<Registry>;
 /**
  * Save the registry atomically.
  * Writes to a temp file first, then renames to prevent partial reads.
+ * The caller must already hold `withRegistryLock`; the explicit name keeps
+ * future mutation paths from silently bypassing cross-process serialization.
  */
-export declare function saveRegistry(registryPath: string, registry: Registry): Promise<void>;
+export declare function saveRegistryUnderLock(registryPath: string, registry: Registry): Promise<void>;
+/**
+ * Serialize registry mutations both within this process and across CLI/daemon
+ * processes. Callers that perform destructive work from a registry snapshot
+ * (notably `prune`) may hold the same lock for their whole transaction.
+ */
+export declare function withRegistryLock<T>(registryPath: string, work: () => Promise<T>): Promise<T>;
 /**
  * Register or update a repo in the registry.
  */

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

@@ -1 +1 @@
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+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAItD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;;;GAKG;AACH,wBAAsB,qBAAqB,CACzC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AAgKD;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,CAAC,EAAE,YAAY,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAc5F;AAED;;GAEG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,QAAQ,GACb,OAAO,CAAC,IAAI,CAAC,CAOf;AAED;;;GAGG;AACH,wBAAsB,OAAO,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAG1B;AAED;;GAEG;AACH,wBAAsB,SAAS,CAC7B,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAGrB;AAED;;GAEG;AACH,wBAAsB,cAAc,CAClC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,EAAE,iBAAiB,GAAG,cAAc,GAAG,YAAY,GAAG,YAAY,CAAC,CAAC,GACjG,OAAO,CAAC,IAAI,CAAC,CASf;AAED;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,OAAO,CAAC,CAalB;AAED;;;;;;;;GAQG;AACH,wBAAsB,yBAAyB,CAC7C,YAAY,EAAE,MAAM,EACpB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,GAAG,IAAI,CAAC,CA6C1D;AA+BD;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CASpD"}

package/dist/storage/registry.js

@@ -1,7 +1,9 @@
-import { readFile } from "node:fs/promises";
-import { readFileSync, existsSync } from "node:fs";
-import { basename, isAbsolute, join, resolve, sep } from "node:path";
+import { randomUUID } from "node:crypto";
+import { link, mkdir, readFile, readdir, rename, unlink, writeFile } from "node:fs/promises";
+import { readFileSync, existsSync, statSync } from "node:fs";
+import { basename, dirname, isAbsolute, join, resolve, sep } from "node:path";
 import { atomicWriteFile } from "./_shared.js";
+import { loadSqliteCtor } from "./sqlite/runtime.js";
 /**
  * Load the multi-repo registry from disk.
  * Returns an empty registry if the file doesn't exist or is invalid.
@@ -22,8 +24,10 @@ export async function loadRegistry(registryPath) {
 /**
  * Save the registry atomically.
  * Writes to a temp file first, then renames to prevent partial reads.
+ * The caller must already hold `withRegistryLock`; the explicit name keeps
+ * future mutation paths from silently bypassing cross-process serialization.
  */
-export async function saveRegistry(registryPath, registry) {
+export async function saveRegistryUnderLock(registryPath, registry) {
     const data = JSON.stringify(registry);
     await atomicWriteFile(registryPath, data);
 }
@@ -43,9 +47,166 @@ export async function saveRegistry(registryPath, registry) {
  * serialises its own writes this way (`writeLocks`); the registry never did.
  */
 const registryWriteLocks = new Map();
-function withRegistryLock(registryPath, work) {
+async function acquireRegistryFileLock(registryPath) {
+    await mkdir(dirname(registryPath), { recursive: true });
+    const DatabaseSync = await loadSqliteCtor();
+    if (!DatabaseSync)
+        return acquireRegistryPortableLock(registryPath);
+    const db = new DatabaseSync(`${registryPath}.lock.db`);
+    const deadline = Date.now() + 5 * 60_000;
+    while (true) {
+        try {
+            db.exec("BEGIN EXCLUSIVE");
+            return {
+                release: async () => {
+                    try {
+                        db.exec("ROLLBACK");
+                    }
+                    catch { /* transaction already closed */ }
+                    db.close();
+                },
+            };
+        }
+        catch (error) {
+            const code = error.code;
+            const message = error instanceof Error ? error.message : String(error);
+            const busy = code === "SQLITE_BUSY" || code === "SQLITE_LOCKED" ||
+                /database is (?:busy|locked)/i.test(message);
+            if (!busy || Date.now() >= deadline) {
+                db.close();
+                throw error;
+            }
+            await new Promise((resolveWait) => setTimeout(resolveWait, 25));
+        }
+    }
+}
+/**
+ * Node 20 has no `node:sqlite`, but remains a supported JSON-backend runtime.
+ * An atomic hard link provides the same cross-process exclusion there. The
+ * candidate file is complete before it can become the public lock path, so
+ * contenders never observe the mkdir/write ownership gap that a lock directory
+ * would have. A crashed owner is reclaimed only after its PID is gone.
+ */
+async function acquireRegistryPortableLock(registryPath) {
+    // Distinct from the SQLite `.lock.db` and from any historical lock-directory
+    // experiment, so a stale artifact cannot change the file-lock semantics.
+    const lockPath = `${registryPath}.lock.file`;
+    const deadline = Date.now() + 5 * 60_000;
+    const token = randomUUID();
+    const candidatePath = `${lockPath}.candidate-${process.pid}-${token}`;
+    await cleanupAbandonedLockCandidates(lockPath);
+    await writeFile(candidatePath, JSON.stringify({ pid: process.pid, token }), { encoding: "utf8", flag: "wx" });
+    try {
+        while (true) {
+            try {
+                await link(candidatePath, lockPath);
+                return {
+                    release: async () => {
+                        const owner = await readRegistryLockOwner(lockPath);
+                        if (owner?.token !== token)
+                            return;
+                        try {
+                            await unlink(lockPath);
+                        }
+                        catch (error) {
+                            if (error.code !== "ENOENT")
+                                throw error;
+                        }
+                    },
+                };
+            }
+            catch (error) {
+                if (error.code !== "EEXIST")
+                    throw error;
+                if (await registryLockIsAbandoned(lockPath)) {
+                    const tombstone = `${lockPath}.stale-${process.pid}-${randomUUID()}`;
+                    try {
+                        await rename(lockPath, tombstone);
+                        await unlink(tombstone);
+                        continue;
+                    }
+                    catch (reapError) {
+                        const code = reapError.code;
+                        if (code !== "ENOENT")
+                            throw reapError;
+                    }
+                }
+                if (Date.now() >= deadline) {
+                    throw new Error(`Timed out waiting for registry lock: ${registryPath}`);
+                }
+                await new Promise((resolveWait) => setTimeout(resolveWait, 25));
+            }
+        }
+    }
+    finally {
+        await unlink(candidatePath).catch(() => undefined);
+    }
+}
+async function cleanupAbandonedLockCandidates(lockPath) {
+    const parent = dirname(lockPath);
+    const prefix = `${basename(lockPath)}.candidate-`;
+    let names;
+    try {
+        names = await readdir(parent);
+    }
+    catch {
+        return;
+    }
+    for (const name of names) {
+        if (!name.startsWith(prefix))
+            continue;
+        const pid = Number.parseInt(name.slice(prefix.length).split("-", 1)[0] ?? "", 10);
+        if (Number.isInteger(pid) && !processIsAlive(pid)) {
+            await unlink(join(parent, name)).catch(() => undefined);
+        }
+    }
+}
+async function readRegistryLockOwner(lockPath) {
+    try {
+        const parsed = JSON.parse(await readFile(lockPath, "utf8"));
+        return Number.isInteger(parsed.pid) && typeof parsed.token === "string"
+            ? { pid: parsed.pid, token: parsed.token }
+            : null;
+    }
+    catch {
+        return null;
+    }
+}
+async function registryLockIsAbandoned(lockPath) {
+    const owner = await readRegistryLockOwner(lockPath);
+    // A valid lock is always published from a complete candidate file. Invalid
+    // or temporarily unreadable metadata is therefore fail-closed: do not reap
+    // something whose dead owner cannot be proved.
+    return owner !== null && !processIsAlive(owner.pid);
+}
+function processIsAlive(pid) {
+    if (pid <= 0)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (error) {
+        return error.code === "EPERM";
+    }
+}
+/**
+ * Serialize registry mutations both within this process and across CLI/daemon
+ * processes. Callers that perform destructive work from a registry snapshot
+ * (notably `prune`) may hold the same lock for their whole transaction.
+ */
+export function withRegistryLock(registryPath, work) {
     const prev = registryWriteLocks.get(registryPath) ?? Promise.resolve();
-    const next = prev.then(work, work);
+    const lockedWork = async () => {
+        const fileLock = await acquireRegistryFileLock(registryPath);
+        try {
+            return await work();
+        }
+        finally {
+            await fileLock.release();
+        }
+    };
+    const next = prev.then(lockedWork, lockedWork);
     // Swallow on the chain only — the caller still sees its own rejection.
     registryWriteLocks.set(registryPath, next.then(() => undefined, () => undefined));
     return next;
@@ -58,7 +219,7 @@ export async function registerRepo(registryPath, meta) {
         const registry = await loadRegistry(registryPath);
         registry.repos[meta.name] = meta;
         registry.updated_at = Date.now();
-        await saveRegistry(registryPath, registry);
+        await saveRegistryUnderLock(registryPath, registry);
     });
 }
 /**
@@ -87,7 +248,7 @@ export async function updateRepoMeta(registryPath, repoName, updates) {
             return;
         Object.assign(existing, updates);
         registry.updated_at = Date.now();
-        await saveRegistry(registryPath, registry);
+        await saveRegistryUnderLock(registryPath, registry);
     });
 }
 /**
@@ -102,7 +263,7 @@ export async function removeRepo(registryPath, name) {
         }
         delete registry.repos[name];
         registry.updated_at = Date.now();
-        await saveRegistry(registryPath, registry);
+        await saveRegistryUnderLock(registryPath, registry);
         return true;
     });
 }
@@ -215,6 +376,17 @@ function isAncestorOrEqual(ancestor, descendant) {
  * through silently to the next step — derivation must never throw.
  */
 export function getRepoName(repoRoot) {
+    const worktree = linkedWorktree(repoRoot);
+    // Base name from the MAIN checkout, not from the worktree: a linked worktree has no
+    // `.git/config` of its own (the config lives in the main repo), so deriving locally would fall
+    // through to the worktree's own basename and every worktree of one repo would get an unrelated
+    // name. Taking the base from the main checkout keeps them grouped under one prefix and differing
+    // only by the suffix — which is what makes the set readable in `list_repos`.
+    if (worktree)
+        return `${baseRepoName(worktree.mainRoot)}@${worktree.name}`;
+    return baseRepoName(repoRoot);
+}
+function baseRepoName(repoRoot) {
     const override = readNameOverride(repoRoot);
     if (override)
         return override;
@@ -223,6 +395,58 @@ export function getRepoName(repoRoot) {
         return `local/${fromGit}`;
     return `local/${basename(repoRoot)}`;
 }
+/**
+ * The git worktree identifier when `repoRoot` is a LINKED worktree, else null.
+ *
+ * Every one of the three name sources above collapses a repo's worktrees onto a single name, and
+ * the registry is keyed by name — so the last one indexed silently evicts the rest. Measured on
+ * this machine: `tgm-survey-platform` has **36 worktrees**, all carrying the same TRACKED
+ * `.codesift.json` (`{"name":"tgm-survey-platform"}`), so 35 registry entries were being
+ * overwritten. The override file is documented as the escape hatch FOR collisions; committing it
+ * makes it the cause of one, because git checks it out into every worktree.
+ *
+ * `git remote.origin.url` collapses them for the same reason (worktrees share the remote), and
+ * even the basename fallback collides whenever two worktrees are named alike under different
+ * parents.
+ *
+ * This is the H19 hazard as a persistent condition rather than a transient one: an agent working
+ * in one worktree resolves the repo by name and gets whichever tree registered last. Disambiguating
+ * here fixes all three sources at once, because it is applied to the result rather than to any of
+ * them.
+ *
+ * Detection is the presence of a `.git` FILE (linked worktrees get a file containing
+ * `gitdir: …/.git/worktrees/<name>`; a main checkout gets a directory). The trailing segment is
+ * git's own worktree name, which git already guarantees unique within the repository — safer than
+ * the directory basename, which is not.
+ */
+function linkedWorktree(repoRoot) {
+    const dotGit = join(repoRoot, ".git");
+    try {
+        if (!statSync(dotGit).isFile())
+            return null; // main checkout, or no git at all
+        const pointer = readFileSync(dotGit, "utf-8").trim();
+        const match = pointer.match(/^gitdir:\s*(.+)$/m);
+        if (!match?.[1])
+            return null;
+        const raw = match[1].trim().replace(/[/\\]+$/, "");
+        // `gitdir:` is normally absolute but git permits a relative pointer.
+        const gitdir = isAbsolute(raw) ? raw : resolve(repoRoot, raw);
+        // Only a worktree pointer qualifies. Submodules also use a `.git` file, and their gitdir
+        // points at `…/.git/modules/<name>` — a submodule is a different repository with its own
+        // remote, so it already gets a distinct name and must not be suffixed onto its parent's.
+        const split = gitdir.split(/[/\\]\.git[/\\]worktrees[/\\]/);
+        if (split.length !== 2)
+            return null;
+        const mainRoot = split[0];
+        const name = split[1]?.split(/[/\\]/)[0];
+        if (!mainRoot || !name)
+            return null;
+        return { name, mainRoot };
+    }
+    catch {
+        return null; // derivation must never throw
+    }
+}
 function readNameOverride(repoRoot) {
     const overridePath = join(repoRoot, ".codesift.json");
     if (!existsSync(overridePath))

package/dist/storage/registry.js.map

@@ -1 +1 @@
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package/dist/storage/shared-embedding-cache.d.ts

@@ -1,3 +1,13 @@
+/**
+ * Basename of the cache file this build reads and writes.
+ *
+ * Exported so `prune` can reclaim SUPERSEDED versions without hard-coding a name
+ * that would drift on the next format bump: it deletes every `shared-embeddings.*`
+ * that is not this one. A format bump otherwise strands the old file forever —
+ * nothing opens it and nothing deletes it, because it has no hash prefix for the
+ * artifact sweep to match (1.05 GB measured after the v1→v2 bump).
+ */
+export declare function currentSharedCacheFilename(): string;
 /**
  * Key for a piece of text under a specific model.
  *
@@ -11,14 +21,24 @@ export declare function contentKey(model: string, dimensions: number, text: stri
 /**
  * Read the cache into memory once per process.
  *
- * Missing file, unreadable line, malformed JSON: all skipped. A cache that
- * cannot be read must degrade into "compute it again", never into an error —
- * it is an optimization, and a broken one has to stay invisible.
+ * Missing file, truncated tail, impossible dimension: all skipped. A cache that
+ * cannot be read must degrade into "compute it again", never into an error — it
+ * is an optimization, and a broken one has to stay invisible.
+ *
+ * A torn final record is the expected failure, not an exotic one: a writer
+ * killed mid-append leaves one. Reading stops at the first record that does not
+ * fit in the remaining bytes and keeps everything before it.
  */
 export declare function loadSharedCache(): Promise<Map<string, Float32Array>>;
 /**
  * Append new vectors. Both the file and the in-memory map are updated, so a
  * second repo indexed in the same process hits memory rather than disk.
+ *
+ * Entries already present are skipped: v1 appended unconditionally and 11.3% of
+ * its lines were repeats of a key it already held. Dedup happens against the
+ * in-memory map, so it is exact within a process and best-effort across them —
+ * which is the same guarantee append-only gave before, at a fraction of the
+ * bytes.
  */
 export declare function appendSharedCache(entries: Array<{
     key: string;

package/dist/storage/shared-embedding-cache.d.ts.map

@@ -1 +1 @@
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