codesift-mcp 0.12.0 → 0.14.0

package/dist/storage/index-store.js

@@ -1,14 +1,115 @@
 import { readFile } from "node:fs/promises";
+import { statSync } from "node:fs";
 import { join } from "node:path";
 import { createHash } from "node:crypto";
 import { atomicWriteFile } from "./_shared.js";
+import { isSqliteAvailable, loadIndexSqlite, saveIndexSqlite, saveIncrementalSqlite, removeFileFromIndexSqlite, getFileEntrySqlite, getDataVersion, importLegacyIndexIfEmpty, classifyStorageError, IndexStorageError, loadIndexSummarySqlite, } from "./sqlite-index-store.js";
+import { indexFootprintBytes } from "./index-footprint.js";
+import { indexCacheMemBudgetBytes } from "../config.js";
+/** Bounded by entry count, not bytes: a summary holds no symbols, so it cannot dominate the heap
+ *  the way a materialised index can. */
+const MAX_CACHED_SUMMARIES = 16;
+const summaryCache = new Map();
+function copySummary(summary) {
+    const out = { ...summary, files: [...summary.files] };
+    if (summary.workspaces !== undefined)
+        out.workspaces = [...summary.workspaces];
+    return out;
+}
+export function resetSummaryCacheForTesting() {
+    summaryCache.clear();
+}
 /** Serialize concurrent writes to the same index path. */
 const writeLocks = new Map();
+/**
+ * Which on-disk format to use.
+ *
+ * `CODESIFT_INDEX_BACKEND=json` pins the legacy path (the documented rollback);
+ * `=sqlite` demands the new one and fails loudly if `node:sqlite` is missing, so a CI run
+ * cannot quietly exercise the wrong backend. Unset auto-detects, which is what keeps the
+ * `engines: >=20` floor honest: Node 20 has no `node:sqlite` and simply stays on JSON.
+ *
+ * Read from the environment here rather than `config.ts` because the choice must be
+ * resolvable from the short-lived `codesift postindex-file` hook process too, which never
+ * builds a full config.
+ */
+let backendPromise;
+export async function resolveIndexBackend() {
+    backendPromise ??= computeIndexBackend();
+    return backendPromise;
+}
+async function computeIndexBackend() {
+    const explicit = process.env["CODESIFT_INDEX_BACKEND"];
+    if (explicit === "json")
+        return "json";
+    if (explicit === "sqlite") {
+        if (!(await isSqliteAvailable())) {
+            throw new Error("CODESIFT_INDEX_BACKEND=sqlite but node:sqlite is unavailable (requires Node >= 22.5)");
+        }
+        return "sqlite";
+    }
+    return (await isSqliteAvailable()) ? "sqlite" : "json";
+}
+export function resetIndexBackendForTesting() {
+    backendPromise = undefined;
+}
+/** `<hash>.index.json` -> `<hash>.index.db`, so both formats sit side by side and the JSON
+ *  stays available as the rollback artifact. */
+export function sqlitePathFor(indexPath) {
+    return indexPath.endsWith(".json")
+        ? `${indexPath.slice(0, -".json".length)}.db`
+        : `${indexPath}.db`;
+}
+/** Guards one-time JSON->SQLite migration per index path. */
+const migrations = new Map();
+/**
+ * Bring an existing JSON index across on first touch.
+ *
+ * Deliberately non-destructive: the source `.json` is left in place. Deleting it would make
+ * `CODESIFT_INDEX_BACKEND=json` a one-way door, and the whole point of shipping a rollback
+ * switch is that it still has something to roll back to.
+ */
+async function ensureSqliteMigrated(indexPath, dbPath) {
+    const inFlight = migrations.get(dbPath);
+    if (inFlight)
+        return inFlight;
+    const run = (async () => {
+        if ((await loadIndexSqlite(dbPath)) !== null)
+            return; // already migrated
+        const legacy = await loadJsonIndex(indexPath);
+        // importLegacyIndexIfEmpty re-checks emptiness under the write lock, so a second
+        // process that raced us here imports nothing instead of overwriting our rows.
+        if (legacy)
+            await importLegacyIndexIfEmpty(dbPath, legacy);
+    })();
+    migrations.set(dbPath, run);
+    try {
+        await run;
+    }
+    catch (err) {
+        // A failed migration is retried, not remembered as done — and we do NOT re-read the same
+        // failing database to decide that. Probing it again inside a `finally` would hit an
+        // already-struggling store a second time AND, if that probe throws too, JS try/finally
+        // semantics would replace the original error with the second one.
+        migrations.delete(dbPath);
+        throw err;
+    }
+    migrations.set(dbPath, Promise.resolve());
+}
+export function resetMigrationCacheForTesting() {
+    migrations.clear();
+}
 /**
  * Save a code index atomically.
  * Writes to a temp file first, then renames to prevent partial reads.
  */
-export async function saveIndex(indexPath, index) {
+export async function saveIndex(indexPath, index, opts) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await saveIndexSqlite(dbPath, index, opts);
+        invalidateIndexCache(dbPath);
+        return;
+    }
     const data = JSON.stringify(index);
     await atomicWriteFile(indexPath, data);
 }
@@ -23,24 +124,290 @@ export async function saveIndex(indexPath, index) {
  * where version enforcement would cause spurious reindexes.
  */
 export async function loadIndex(indexPath, currentVersions) {
-    try {
-        const raw = await readFile(indexPath, "utf-8");
-        const parsed = JSON.parse(raw);
-        if (!isValidIndex(parsed)) {
+    const index = await readIndex(indexPath);
+    if (!index)
+        return null;
+    if (currentVersions && !isExtractorVersionCurrent(index, currentVersions))
+        return null;
+    return index;
+}
+/**
+ * One file's `files[]` entry.
+ *
+ * This is the accessor ADR-003 exists for. `file-indexer` needs a single file's `mtime_ms`
+ * and `symbol_count` to decide whether an edit changed anything, and used to obtain them by
+ * loading the entire index — a 262 MB parse on tgm-survey-platform, paid on the first touch
+ * of every file, in a hook process that exits immediately afterwards and so can never reuse
+ * the result. Under SQLite it is one indexed row.
+ *
+ * The JSON backend keeps the old cost; there is no way to read one record out of a blob.
+ */
+export async function getFileEntry(indexPath, filePath) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await ensureSqliteMigrated(indexPath, dbPath);
+        return getFileEntrySqlite(dbPath, filePath);
+    }
+    const index = await loadJsonIndex(indexPath);
+    return index?.files.find((f) => f.path === filePath);
+}
+/**
+ * Bounded, LRU by insertion order. A materialised index is the largest object this process
+ * holds — the JSON equivalent is 262 MB on tgm-survey-platform — and `codesift serve` is a
+ * long-lived daemon that touches many repos. An unbounded map here would have been the one
+ * cache in this codebase without a ceiling, next to an embedding cache that is explicitly
+ * RAM-budgeted (`CODESIFT_MAX_EMBEDDING_MEM_MB`); that asymmetry is how the OOM reports
+ * documented in CLAUDE.md started.
+ */
+// `|| 3` would be wrong here: an operator setting 0 to minimise memory would get 3, because
+// 0 is falsy. Only a non-numeric value should fall back.
+const MAX_CACHED_INDEXES = (() => {
+    const raw = process.env["CODESIFT_MAX_CACHED_INDEXES"];
+    const parsed = raw === undefined ? 3 : Number(raw);
+    return Math.max(1, Number.isNaN(parsed) ? 3 : parsed);
+})();
+const indexCache = new Map();
+function cachedBytes() {
+    let total = 0;
+    for (const entry of indexCache.values())
+        total += indexFootprintBytes(entry.index);
+    return total;
+}
+function cacheIndex(dbPath, entry) {
+    // Re-insert to move to the most-recent end of Map iteration order.
+    indexCache.delete(dbPath);
+    indexCache.set(dbPath, entry);
+    const budget = indexCacheMemBudgetBytes();
+    // Evict oldest-first on EITHER bound. The count cap alone let three repos of any size sit
+    // resident, and index sizes span two orders of magnitude — the measured tgm-survey-platform
+    // index is 411 MB against a few MB for a small repo, so "three indexes" was a ceiling only in
+    // name. The byte bound is the real one; the count cap stays as a cheap upper limit on entries.
+    //
+    // The running total is decremented per eviction rather than re-summed in the loop condition.
+    // `MAX_CACHED_INDEXES` has a floor but no ceiling (`CODESIFT_MAX_CACHED_INDEXES` is operator
+    // input), and re-summing would make each insert O(n²) in exactly the many-repo daemon this
+    // budget was written for.
+    let total = cachedBytes();
+    while (indexCache.size > 1 && (indexCache.size > MAX_CACHED_INDEXES || total > budget)) {
+        const oldest = indexCache.entries().next();
+        if (oldest.done)
+            break;
+        const [key, entry] = oldest.value;
+        total -= indexFootprintBytes(entry.index);
+        indexCache.delete(key);
+    }
+    // `size > 1` above deliberately keeps the entry just inserted even when it alone exceeds the
+    // budget. Evicting it would mean re-reading the same index on the very next call and evicting
+    // it again — an unbounded reload loop that costs far more than the memory it reclaims. A repo
+    // bigger than the whole budget is a reason to raise CODESIFT_MAX_INDEX_CACHE_MB, not to stop
+    // caching it.
+}
+/**
+ * Detach the two arrays callers actually touch.
+ *
+ * A bare `{...index}` only stops a caller REASSIGNING `files`/`symbols`; an in-place
+ * `push`/`sort`/`splice` would still hit the array the cache holds — and `data_version`
+ * cannot see an in-memory mutation, so the corruption would survive every later hit. The
+ * elements stay shared (symbols are treated as immutable records); this copies the two
+ * array containers, which is the boundary that was actually being crossed.
+ */
+function copyIndex(index) {
+    return { ...index, files: [...index.files], symbols: [...index.symbols] };
+}
+function invalidateIndexCache(dbPath) {
+    indexCache.delete(dbPath);
+    // Our own writes do not move `data_version`, so the summary must be dropped explicitly too —
+    // otherwise a save would leave `index_status` reporting the pre-write counts indefinitely.
+    summaryCache.delete(dbPath);
+}
+export function resetIndexCacheForTesting() {
+    indexCache.clear();
+}
+export function getIndexCacheSizeForTesting() {
+    return indexCache.size;
+}
+export function getIndexCacheBytesForTesting() {
+    return cachedBytes();
+}
+/**
+ * Read an index's files and metadata WITHOUT constructing its symbols (ADR-004 stage 2).
+ *
+ * On the SQLite backend this skips the object graph entirely. On JSON there is nothing to skip —
+ * the format forces a whole-document parse — so this is parity, not a speedup, and it exists so
+ * callers can be written once against the narrow shape rather than branching on the backend.
+ */
+export async function loadIndexSummary(indexPath) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await ensureSqliteMigrated(indexPath, dbPath);
+        // Cached on the same `data_version` signal as the full index. Without this a repo whose only
+        // traffic is `index_status` re-opened a connection and re-read the whole files table on every
+        // call, while its `getCodeIndex` sibling was served from memory — an asymmetry with no reason
+        // behind it. A summary is small (3 MB against 349 MB on the measured index), so this is not
+        // budgeted against `CODESIFT_MAX_INDEX_CACHE_MB`; it is bounded by entry count instead.
+        const dataVersion = await getDataVersion(dbPath);
+        const cached = summaryCache.get(dbPath);
+        if (cached && cached.dataVersion === dataVersion) {
+            summaryCache.delete(dbPath);
+            summaryCache.set(dbPath, cached); // move to the recent end (LRU, as in cacheIndex)
+            return copySummary(cached.summary);
+        }
+        const summary = await loadIndexSummarySqlite(dbPath);
+        if (summary === null)
             return null;
+        summaryCache.set(dbPath, { summary, dataVersion });
+        while (summaryCache.size > MAX_CACHED_SUMMARIES) {
+            const oldest = summaryCache.keys().next();
+            if (oldest.done)
+                break;
+            summaryCache.delete(oldest.value);
+        }
+        // Copy on the miss path too, for the same reason `readIndex` does: handing back the stored
+        // object lets the first caller mutate the entry every later reader is about to be given.
+        return copySummary(summary);
+    }
+    warnIfRollbackIsStale(indexPath);
+    const index = await loadJsonIndex(indexPath);
+    return index === null ? null : summariseIndex(index);
+}
+/**
+ * Project a fully-loaded index onto the narrow shape, dropping the symbols array.
+ *
+ * `files` is COPIED, not aliased. This function's main caller projects an index held in the
+ * `codeIndexes` cache, so handing back the live array would let one caller's `sort`/`splice`
+ * rewrite what every later reader is given — the exact boundary `copyIndex` above exists to
+ * defend, reached by a different route. `workspaces` is copied for the same reason.
+ */
+export function summariseIndex(index) {
+    const summary = {
+        repo: index.repo,
+        root: index.root,
+        files: index.files === undefined ? [] : [...index.files],
+        created_at: index.created_at,
+        updated_at: index.updated_at,
+        symbol_count: index.symbol_count,
+        file_count: index.file_count,
+    };
+    if (index.extractor_version !== undefined)
+        summary.extractor_version = index.extractor_version;
+    if (index.workspaces !== undefined)
+        summary.workspaces = [...index.workspaces];
+    // `files` is required on CodeIndex, so the guard above is unreachable through the typed path —
+    // but this projects objects that also arrive from JSON on disk, where nothing enforces the type,
+    // and the cache-hit call site sits outside its caller's try/catch. A throw there would surface as
+    // a crash on a status call, which is a worse answer than an empty file list.
+    if (index.lossy_migration === true)
+        summary.lossy_migration = true;
+    return summary;
+}
+/** Backend-agnostic read, without version enforcement. */
+async function readIndex(indexPath) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await ensureSqliteMigrated(indexPath, dbPath);
+        const dataVersion = await getDataVersion(dbPath);
+        const cached = indexCache.get(dbPath);
+        if (cached && cached.dataVersion === dataVersion) {
+            // Re-insert on HIT too, or the eviction order is FIFO-by-first-load rather than LRU:
+            // the hottest repo would be evicted the moment an (N+1)th repo is touched, while a
+            // repo read once and never again outlives it. That thrashes exactly the working set
+            // the cache exists to keep warm.
+            cacheIndex(dbPath, cached);
+            return copyIndex(cached.index);
         }
-        if (currentVersions && !isExtractorVersionCurrent(parsed, currentVersions)) {
+        const index = await loadIndexSqlite(dbPath);
+        if (!index)
             return null;
+        cacheIndex(dbPath, { index, dataVersion });
+        // Copy on the miss path too: returning the freshly-cached object itself would let the
+        // very first caller mutate the entry every later reader is about to be handed.
+        return copyIndex(index);
+    }
+    warnIfRollbackIsStale(indexPath);
+    return loadJsonIndex(indexPath);
+}
+/**
+ * Warn when the JSON backend is serving a snapshot that SQLite has since moved past.
+ *
+ * The rollback switch keeps the `.json` untouched, which is what makes rolling back possible
+ * — and also means that after a repo has run on SQLite for a while, the JSON is a frozen
+ * snapshot from migration day. Falling back to it then answers every query from a stale index
+ * with no error and no empty result: the shape is valid, the extractor versions still match,
+ * it is simply old. That is the worst failure mode we have (confidently wrong), so it gets a
+ * loud one-time line rather than silence.
+ */
+const staleRollbackWarned = new Set();
+function warnIfRollbackIsStale(indexPath) {
+    if (staleRollbackWarned.has(indexPath))
+        return;
+    try {
+        // Mark only once a real comparison happened. Marking up front would permanently silence
+        // the warning for a long-lived JSON-pinned process that read this repo before any `.db`
+        // existed — precisely the process that most needs telling when one appears later.
+        const dbStat = statSync(sqlitePathFor(indexPath));
+        const jsonStat = statSync(indexPath);
+        staleRollbackWarned.add(indexPath);
+        if (dbStat.mtimeMs <= jsonStat.mtimeMs)
+            return;
+        const ageHours = Math.round((dbStat.mtimeMs - jsonStat.mtimeMs) / 3_600_000);
+        console.error(`[codesift] WARNING: reading the legacy JSON index at ${indexPath}, but a SQLite index ` +
+            `updated ~${ageHours}h more recently exists alongside it. Every answer from this repo ` +
+            `is from the pre-rollback snapshot. Run index_folder to rebuild the JSON index, or ` +
+            `unset CODESIFT_INDEX_BACKEND to go back to SQLite.`);
+    }
+    catch {
+        /* no .db, or unreadable — nothing to compare against, so nothing to warn about */
+    }
+}
+export function resetStaleRollbackWarningForTesting() {
+    staleRollbackWarned.clear();
+}
+/**
+ * Codes that genuinely mean "there is no index file here". Everything else that `readFile` can
+ * fail with — EISDIR, ENOTDIR, ENAMETOOLONG, ELOOP, platform-specific I/O errors — describes a
+ * path that is wrong or unreadable, not a repo that was never indexed. Reporting those as
+ * absence is the same misdiagnosis this change exists to remove, one layer down.
+ */
+const ABSENCE_CODES = new Set(["ENOENT", "ENOTDIR_PARENT"]);
+function nonAbsenceReadCode(err) {
+    const code = typeof err === "object" && err !== null ? err.code : undefined;
+    // No recognisable code at all: this is NOT evidence of absence. Only an explicit ENOENT is.
+    // Defaulting the unknown case to "nothing indexed here" is how a real fault becomes a
+    // confident empty answer — the whole failure mode being removed.
+    if (typeof code !== "string")
+        return "UNKNOWN_READ_ERROR";
+    return ABSENCE_CODES.has(code) ? null : code;
+}
+/**
+ * The legacy path, kept intact: it is both the Node 20 backend and the rollback target.
+ *
+ * ENOENT is absence and stays `null`; a malformed document is also `null` (an invalid index is
+ * rebuildable, which is the historical contract). But EACCES/EIO/EBUSY mean the file exists and
+ * we simply could not read it — reporting that as "no index" is how a permissions problem gets
+ * misdiagnosed as an unindexed repo.
+ */
+async function loadJsonIndex(indexPath) {
+    let raw;
+    try {
+        raw = await readFile(indexPath, "utf-8");
+    }
+    catch (err) {
+        const code = classifyStorageError(err) ?? nonAbsenceReadCode(err);
+        if (code !== null) {
+            throw new IndexStorageError(`index storage at ${indexPath} is unreadable (${code}): ${err instanceof Error ? err.message : String(err)}`, code, indexPath, { cause: err });
         }
+        return null; // ENOENT and friends: nothing indexed here
+    }
+    try {
+        const parsed = JSON.parse(raw);
+        if (!isValidIndex(parsed))
+            return null;
         return parsed;
     }
     catch {
-        return null;
+        return null; // malformed JSON is a rebuildable index, not a storage fault
     }
 }
-/** All languages whose stored `extractor_version` entry does not match
- *  `currentVersions`, applying the same tolerances as `loadIndexOrStale`
- *  (newly added keys with no files in that language are skipped). */
 export function collectExtractorVersionMismatches(index, currentVersions) {
     const stored = index.extractor_version ?? {};
     const storedKeys = Object.keys(stored);
@@ -96,10 +463,23 @@ export function collectExtractorVersionMismatches(index, currentVersions) {
  * to `loadIndex(...)` returning null. Callers must still handle null (no
  * structured error) for those cases. */
 export async function loadIndexOrStale(indexPath, currentVersions) {
+    let parsed;
     try {
-        const raw = await readFile(indexPath, "utf-8");
-        const parsed = JSON.parse(raw);
-        if (!isValidIndex(parsed))
+        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) {
@@ -241,6 +621,15 @@ function enqueueIndexMutation(indexPath, missing, apply) {
  * Serialized per indexPath to prevent read-modify-write races.
  */
 export async function saveIncremental(indexPath, updatedFile, newSymbols, fileEntry) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await ensureSqliteMigrated(indexPath, dbPath);
+        // No mutation batching here on purpose: batching exists to amortise a whole-blob
+        // rewrite, and this backend writes one file's rows inside a transaction instead.
+        await saveIncrementalSqlite(dbPath, updatedFile, newSymbols, fileEntry);
+        invalidateIndexCache(dbPath);
+        return;
+    }
     return enqueueIndexMutation(indexPath, "throw", (existing) => {
         const filtered = existing.symbols.filter((symbol) => symbol.file !== updatedFile);
         const merged = [...filtered, ...newSymbols];
@@ -261,6 +650,13 @@ export async function saveIncremental(indexPath, updatedFile, newSymbols, fileEn
  * Serialized per indexPath to prevent read-modify-write races.
  */
 export async function removeFileFromIndex(indexPath, deletedFile) {
+    if ((await resolveIndexBackend()) === "sqlite") {
+        const dbPath = sqlitePathFor(indexPath);
+        await ensureSqliteMigrated(indexPath, dbPath);
+        await removeFileFromIndexSqlite(dbPath, deletedFile);
+        invalidateIndexCache(dbPath);
+        return;
+    }
     return enqueueIndexMutation(indexPath, "skip", (existing) => {
         const hadSymbols = existing.symbols.some((s) => s.file === deletedFile);
         const hadFile = existing.files.some((f) => f.path === deletedFile);

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

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

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAGtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AA2BD;;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,CAQpD"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAGtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AA2BD;;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

@@ -1,5 +1,5 @@
 import { readFile } from "node:fs/promises";
-import { readFileSync, existsSync } from "node:fs";
+import { readFileSync, existsSync, statSync } from "node:fs";
 import { basename, isAbsolute, join, resolve, sep } from "node:path";
 import { atomicWriteFile } from "./_shared.js";
 /**
@@ -215,6 +215,17 @@ 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 +234,58 @@ 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))