@indigoai-us/hq-cloud 6.14.18 → 6.14.20

package/dist/qmd-reindex.js

@@ -24,19 +24,258 @@
  *
  * The index itself is never synced — it is large, binary, and embeds absolute
  * local paths. Only its *freshness* is automated here.
+ *
+ * ## Corruption safety (feedback_b9a369ff)
+ *
+ * The qmd store (`.qmd/index.sqlite`, backed by a sqlite-vec virtual table) was
+ * being corrupted on the vector side (`content_vectors` / `vectors_vec_rowids`)
+ * because TWO uncoordinated writers raced on it: this post-sync reindex and an
+ * interactive session's own qmd maintenance (e.g. a skill's `qmd embed`). Two
+ * defects compounded:
+ *   1. A hard 120s `spawnSync` timeout that KILLED a long `qmd update`/`embed`
+ *      mid-write, tearing down the process between vector-table writes.
+ *   2. No cross-process serialization, so an interactive `qmd embed` and a
+ *      runner-spawned `qmd update` overlapped with near certainty.
+ *
+ * The mitigations here, all inside the runner so every teammate gets them on
+ * their next sync:
+ *   - The exec timeout is raised substantially so a legitimate long pass is no
+ *     longer killed mid-write in the first place. A timed-out pass is treated as
+ *     "not done" (left dirty, retried next cycle) and NEVER advances to embed.
+ *     That not-done handling — together with the writer serialization below — is
+ *     the real protection; the signal used for the (now rare) kill is secondary.
+ *     When the bound does fire the child is sent SIGINT rather than the default
+ *     SIGTERM, but qmd 2.5.3 traps both identically (each just restores the
+ *     cursor and exits), so this is only the same clean exit path qmd takes on
+ *     Ctrl-C — not a guarantee the in-flight SQLite write unwinds.
+ *   - A shared advisory lock at `<hqRoot>/.qmd/.reindex.lock` serializes qmd
+ *     writers. The runner takes it before touching qmd and SKIPS the cycle (and
+ *     marks the tree dirty so the next sync retries) when another writer holds
+ *     it. The lock path sits next to the DB so interactive HQ qmd maintenance
+ *     can honor the same rendezvous.
+ *   - Corruption is detected cheaply from qmd's own output (the SQLITE_CORRUPT
+ *     signature). On detection the corrupt DB files are quarantined aside (moved
+ *     to `index.sqlite.corrupt-<ts>`, never deleted) and the cycle stops writing
+ *     so a clean rebuild happens on the next pass — instead of writing further
+ *     onto an already-damaged store.
  */
 import * as fs from "fs";
 import * as path from "path";
 import { spawnSync } from "child_process";
+/**
+ * Default exec timeout for a single `qmd` invocation. The historical 120s bound
+ * routinely killed `qmd update`/`qmd embed` mid-write on a large index (the HQ
+ * root's `hq` collection alone spans the whole tree), which corrupted the vector
+ * store. 15 minutes comfortably covers a cold or embed-heavy pass, so the bound
+ * effectively stops firing on legitimate work; a genuinely wedged process is
+ * still bounded, and a timed-out pass is treated as not-done (never written
+ * further onto) — see {@link defaultExec} and {@link reindexAfterSync}.
+ */
+export const DEFAULT_QMD_EXEC_TIMEOUT_MS = 900_000;
+/** Resolve the exec timeout, honoring `HQ_QMD_EXEC_TIMEOUT_MS` (ms) if valid. */
+export function resolveExecTimeoutMs(env = process.env) {
+    const raw = env.HQ_QMD_EXEC_TIMEOUT_MS;
+    if (raw !== undefined && raw !== "") {
+        const n = Number(raw);
+        if (Number.isFinite(n) && n > 0)
+            return Math.round(n);
+    }
+    return DEFAULT_QMD_EXEC_TIMEOUT_MS;
+}
 const defaultExec = (args) => {
     const res = spawnSync("qmd", args, {
         encoding: "utf8",
-        // qmd update on a large index can take a while; bound it so a wedged
-        // index never hangs the runner forever.
-        timeout: 120_000,
+        // Bound so a wedged index never hangs the runner forever, but generously —
+        // see DEFAULT_QMD_EXEC_TIMEOUT_MS.
+        timeout: resolveExecTimeoutMs(),
+        // On timeout send SIGINT instead of the default SIGTERM. NOTE: qmd 2.5.3
+        // traps BOTH identically — each handler only restores the cursor and calls
+        // process.exit() — so SIGINT is NOT inherently a graceful transaction
+        // unwind; it is simply the same exit path qmd takes on Ctrl-C. The real
+        // write-safety guarantee is the raised bound above (a kill is now rare) plus
+        // treating a timed-out pass as not-done and never embedding after it (see
+        // reindexAfterSync). SIGINT is kept only so a killed pass exits qmd's normal
+        // way rather than via an unhandled default signal.
+        killSignal: "SIGINT",
+    });
+    const timedOut = res.error != null &&
+        res.error.code === "ETIMEDOUT";
+    return {
+        status: res.status,
+        stdout: res.stdout ?? "",
+        stderr: res.stderr ?? "",
+        timedOut,
+    };
+};
+/** SQLite corruption signature qmd surfaces when the vector store is damaged. */
+const CORRUPTION_SIGNATURE = /SQLITE_CORRUPT|database disk image is malformed/i;
+/** True if a qmd result reports SQLite corruption on stdout or stderr. */
+export function looksCorrupt(r) {
+    return CORRUPTION_SIGNATURE.test(`${r.stdout ?? ""}\n${r.stderr ?? ""}`);
+}
+/**
+ * How long a lock file may sit before a new acquirer treats it as abandoned and
+ * reclaims it, even if its recorded PID can't be probed (e.g. a different user,
+ * or a torn/empty file). Backstops the PID-liveness check for the crash case.
+ */
+const DEFAULT_LOCK_STALE_MS = 30 * 60_000;
+function reindexLockStaleMs(env = process.env) {
+    const raw = env.HQ_QMD_LOCK_STALE_MS;
+    if (raw !== undefined && raw !== "") {
+        const n = Number(raw);
+        if (Number.isFinite(n) && n >= 0)
+            return Math.round(n);
+    }
+    return DEFAULT_LOCK_STALE_MS;
+}
+const NOOP_LOCK = { release() { } };
+// Track locks this process holds so a clean exit/signal removes them; a crash is
+// covered by the stale/PID reclaim path in the acquirer.
+const heldReindexLocks = new Set();
+let reindexExitHookInstalled = false;
+function installReindexExitHookOnce() {
+    if (reindexExitHookInstalled)
+        return;
+    reindexExitHookInstalled = true;
+    process.on("exit", () => {
+        for (const p of heldReindexLocks)
+            unlinkIfOwned(p);
+    });
+}
+/** Is `pid` a live process? ESRCH → dead; EPERM/other → conservatively alive. */
+function pidAlive(pid) {
+    if (!Number.isInteger(pid) || pid <= 0)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (err) {
+        return err?.code !== "ESRCH";
+    }
+}
+/** Unlink `lockPath` only if it still records THIS process as the holder. */
+function unlinkIfOwned(lockPath) {
+    try {
+        const info = JSON.parse(fs.readFileSync(lockPath, "utf8"));
+        if (info?.pid !== process.pid)
+            return;
+    }
+    catch {
+        // Unreadable/torn/already-gone — don't risk clobbering another holder.
+        return;
+    }
+    try {
+        fs.unlinkSync(lockPath);
+    }
+    catch {
+        /* already gone — fine */
+    }
+}
+/**
+ * If the lock at `lockPath` is held by a dead PID or is older than the stale
+ * bound, unlink it so the caller can retry. Returns true when it reclaimed (or
+ * the lock vanished mid-check), false when a live, fresh holder still owns it.
+ */
+function reclaimReindexLockIfStale(lockPath) {
+    let st;
+    try {
+        st = fs.statSync(lockPath);
+    }
+    catch {
+        // Vanished between EEXIST and stat → the holder released; let caller retry.
+        return true;
+    }
+    let holderPid = 0;
+    try {
+        const info = JSON.parse(fs.readFileSync(lockPath, "utf8"));
+        if (typeof info?.pid === "number")
+            holderPid = info.pid;
+    }
+    catch {
+        /* torn/empty lock — fall through to the staleness check */
+    }
+    const dead = holderPid > 0 && !pidAlive(holderPid);
+    const stale = Date.now() - st.mtimeMs > reindexLockStaleMs();
+    if (dead || stale) {
+        try {
+            fs.unlinkSync(lockPath);
+        }
+        catch {
+            // Someone else reclaimed it first; the next create attempt re-evaluates.
+        }
+        return true;
+    }
+    return false;
+}
+const defaultAcquireReindexLock = (lockPath) => {
+    // Escape hatch: a caller that manages exclusion itself can disable the lock.
+    if (process.env.HQ_QMD_REINDEX_LOCK === "0")
+        return NOOP_LOCK;
+    const payload = JSON.stringify({
+        pid: process.pid,
+        startedAt: new Date().toISOString(),
+        command: "hq-cloud qmd-reindex",
     });
-    return { status: res.status, stdout: res.stdout ?? "" };
+    // At most one reclaim + one retry: acquire, or (if stale) reclaim then retry.
+    for (let attempt = 0; attempt < 2; attempt++) {
+        try {
+            fs.mkdirSync(path.dirname(lockPath), { recursive: true });
+            const fd = fs.openSync(lockPath, "wx", 0o600);
+            try {
+                fs.writeSync(fd, payload);
+            }
+            finally {
+                fs.closeSync(fd);
+            }
+            heldReindexLocks.add(lockPath);
+            installReindexExitHookOnce();
+            return {
+                release() {
+                    heldReindexLocks.delete(lockPath);
+                    unlinkIfOwned(lockPath);
+                },
+            };
+        }
+        catch (err) {
+            if (err?.code !== "EEXIST") {
+                // The `.qmd` dir isn't writable (unusual — it holds the DB). Fail OPEN
+                // rather than block the reindex on an infra problem: proceed without the
+                // advisory lock. The corruption guard below is the remaining backstop.
+                return NOOP_LOCK;
+            }
+            // Held. Reclaim iff the holder is dead/stale, then retry once.
+            if (reclaimReindexLockIfStale(lockPath))
+                continue;
+            return null; // live, fresh holder → skip this cycle
+        }
+    }
+    return null;
 };
+const CORRUPTIBLE_DB_FILES = ["index.sqlite", "index.sqlite-wal", "index.sqlite-shm"];
+const defaultQuarantineCorruptIndex = (qmdDir, tsSuffix) => {
+    let movedBase = null;
+    for (const name of CORRUPTIBLE_DB_FILES) {
+        const src = path.join(qmdDir, name);
+        try {
+            if (!fs.existsSync(src))
+                continue;
+            const dest = `${src}.corrupt-${tsSuffix}`;
+            fs.renameSync(src, dest);
+            if (name === "index.sqlite")
+                movedBase = dest;
+        }
+        catch {
+            // Best-effort: move what we can. A file we can't move is left in place;
+            // the corruption guard still prevents further writes this cycle.
+        }
+    }
+    return movedBase;
+};
+/** Filesystem-safe timestamp suffix for a quarantined DB file. */
+function quarantineSuffix(nowMs) {
+    return new Date(nowMs).toISOString().replace(/[:.]/g, "-");
+}
 const DEFAULT_CHANGED_PATH_DEBOUNCE_MS = 60_000;
 /**
  * Reindex qmd for an HQ tree after a sync. Never throws — all failures are
@@ -47,12 +286,17 @@ const DEFAULT_CHANGED_PATH_DEBOUNCE_MS = 60_000;
 export function reindexAfterSync(hqRoot, opts = {}) {
     const exec = opts.exec ?? defaultExec;
     const existsSync = opts.existsSync ?? fs.existsSync;
+    const acquireLock = opts.acquireReindexLock ?? defaultAcquireReindexLock;
+    const quarantine = opts.quarantineCorruptIndex ?? defaultQuarantineCorruptIndex;
     const result = {
         qmdAvailable: false,
         collectionsAdded: [],
         updated: false,
         embedded: false,
         pendingDirty: false,
+        lockBusy: false,
+        timedOut: false,
+        corruptionQuarantined: false,
     };
     try {
         // Guard: only operate on a real HQ tree.
@@ -70,73 +314,106 @@ export function reindexAfterSync(hqRoot, opts = {}) {
         if (!dirtyFromChanges && !registrationMayBeStale && !pendingDirty) {
             return result;
         }
-        // Guard: qmd must be installed. `qmd collection list` doubles as the
-        // availability probe AND the source for which collections already exist.
-        const list = exec(["collection", "list"]);
-        if (list.status !== 0)
-            return result; // qmd absent or errored — no-op
-        result.qmdAvailable = true;
-        const existingCollections = list.stdout;
-        // 1. Auto-register missing company knowledge collections.
-        if (registrationMayBeStale) {
-            const companiesDir = path.join(hqRoot, "companies");
-            const slugs = (opts.readCompanies ?? defaultReadCompanies)(companiesDir);
-            for (const slug of slugs) {
-                const knowledgeDir = path.join(companiesDir, slug, "knowledge");
-                if (!existsSync(knowledgeDir))
-                    continue;
-                const hasMd = (opts.hasIndexableMarkdown ?? defaultHasIndexableMarkdown)(knowledgeDir);
-                if (!hasMd)
-                    continue;
-                // Already registered? qmd collection URIs look like `qmd://<slug>/`.
-                if (existingCollections.includes(`qmd://${slug}/`))
-                    continue;
-                const add = exec(["collection", "add", knowledgeDir, "--name", slug, "--mask", "**/*.md"]);
-                if (add.status === 0) {
-                    exec(["context", "add", `qmd://${slug}`, `Knowledge base for ${slug}.`]);
-                    result.collectionsAdded.push(slug);
-                }
-            }
+        const nowMs = opts.nowMs ?? Date.now();
+        const pendingSinceMs = pendingDirty && typeof state.pendingSinceMs === "number"
+            ? state.pendingSinceMs
+            : nowMs;
+        // Serialize qmd writers. If another writer (this runner from a prior cycle,
+        // or an interactive session's qmd maintenance) holds the lock, SKIP this
+        // cycle and mark the tree dirty so the next sync retries — never write onto
+        // the vector store concurrently (feedback_b9a369ff).
+        const lockPath = path.join(hqRoot, ".qmd", ".reindex.lock");
+        const lock = acquireLock(lockPath);
+        if (!lock) {
+            writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+            result.lockBusy = true;
+            result.pendingDirty = true;
+            return result;
         }
-        // 2. Incremental lexical reindex.
-        const shouldUpdate = dirtyFromChanges || pendingDirty;
-        if (shouldUpdate) {
-            const nowMs = opts.nowMs ?? Date.now();
-            const debounceMs = opts.debounceMs ??
-                (changedPaths === undefined ? 0 : DEFAULT_CHANGED_PATH_DEBOUNCE_MS);
-            const pendingSinceMs = pendingDirty && typeof state.pendingSinceMs === "number"
-                ? state.pendingSinceMs
-                : nowMs;
-            if (debounceMs > 0 && nowMs - pendingSinceMs < debounceMs) {
-                writeState(statePath, {
-                    ...state,
-                    pendingDirty: true,
-                    pendingSinceMs,
-                });
-                result.pendingDirty = true;
+        try {
+            // Guard: qmd must be installed. `qmd collection list` doubles as the
+            // availability probe AND the source for which collections already exist.
+            const list = exec(["collection", "list"]);
+            if (list.status !== 0)
+                return result; // qmd absent or errored — no-op
+            // An already-corrupt store can surface here even on the lexical side.
+            if (looksCorrupt(list)) {
+                handleCorruption(hqRoot, statePath, state, pendingSinceMs, nowMs, quarantine, result);
                 return result;
             }
-            const update = exec(["update"]);
-            result.updated = update.status === 0;
-            if (result.updated) {
-                writeState(statePath, {
-                    pendingDirty: false,
-                    lastSuccessMs: nowMs,
-                });
+            result.qmdAvailable = true;
+            const existingCollections = list.stdout;
+            // 1. Auto-register missing company knowledge collections.
+            if (registrationMayBeStale) {
+                const companiesDir = path.join(hqRoot, "companies");
+                const slugs = (opts.readCompanies ?? defaultReadCompanies)(companiesDir);
+                for (const slug of slugs) {
+                    const knowledgeDir = path.join(companiesDir, slug, "knowledge");
+                    if (!existsSync(knowledgeDir))
+                        continue;
+                    const hasMd = (opts.hasIndexableMarkdown ?? defaultHasIndexableMarkdown)(knowledgeDir);
+                    if (!hasMd)
+                        continue;
+                    // Already registered? qmd collection URIs look like `qmd://<slug>/`.
+                    if (existingCollections.includes(`qmd://${slug}/`))
+                        continue;
+                    const add = exec(["collection", "add", knowledgeDir, "--name", slug, "--mask", "**/*.md"]);
+                    if (add.status === 0) {
+                        exec(["context", "add", `qmd://${slug}`, `Knowledge base for ${slug}.`]);
+                        result.collectionsAdded.push(slug);
+                    }
+                }
             }
-            else {
-                writeState(statePath, {
-                    ...state,
-                    pendingDirty: true,
-                    pendingSinceMs,
-                });
-                result.pendingDirty = true;
+            // 2. Incremental lexical reindex.
+            const shouldUpdate = dirtyFromChanges || pendingDirty;
+            if (shouldUpdate) {
+                const debounceMs = opts.debounceMs ??
+                    (changedPaths === undefined ? 0 : DEFAULT_CHANGED_PATH_DEBOUNCE_MS);
+                if (debounceMs > 0 && nowMs - pendingSinceMs < debounceMs) {
+                    writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+                    result.pendingDirty = true;
+                    return result;
+                }
+                const update = exec(["update"]);
+                if (looksCorrupt(update)) {
+                    handleCorruption(hqRoot, statePath, state, pendingSinceMs, nowMs, quarantine, result);
+                    return result;
+                }
+                if (update.timedOut) {
+                    // Aborted mid-pass by the timeout. Do NOT treat as done and do NOT
+                    // proceed to embed — mark dirty and retry cleanly next cycle.
+                    writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+                    result.timedOut = true;
+                    result.pendingDirty = true;
+                    return result;
+                }
+                result.updated = update.status === 0;
+                if (result.updated) {
+                    writeState(statePath, { pendingDirty: false, lastSuccessMs: nowMs });
+                }
+                else {
+                    writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+                    result.pendingDirty = true;
+                }
+            }
+            // 3. Embeddings only on explicit request.
+            if (opts.embed) {
+                const embed = exec(["embed"]);
+                if (looksCorrupt(embed)) {
+                    handleCorruption(hqRoot, statePath, state, pendingSinceMs, nowMs, quarantine, result);
+                    return result;
+                }
+                if (embed.timedOut) {
+                    writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+                    result.timedOut = true;
+                    result.pendingDirty = true;
+                    return result;
+                }
+                result.embedded = embed.status === 0;
             }
         }
-        // 3. Embeddings only on explicit request.
-        if (opts.embed) {
-            const embed = exec(["embed"]);
-            result.embedded = embed.status === 0;
+        finally {
+            lock.release();
         }
     }
     catch (err) {
@@ -155,6 +432,18 @@ export function reindexAfterSync(hqRoot, opts = {}) {
     }
     return result;
 }
+/**
+ * Quarantine the corrupt DB aside and mark the tree dirty so the NEXT cycle
+ * rebuilds from scratch under the lock, instead of writing further onto an
+ * already-damaged vector store. Mutates `result` in place.
+ */
+function handleCorruption(hqRoot, statePath, state, pendingSinceMs, nowMs, quarantine, result) {
+    const qmdDir = path.join(hqRoot, ".qmd");
+    quarantine(qmdDir, quarantineSuffix(nowMs));
+    writeState(statePath, { ...state, pendingDirty: true, pendingSinceMs });
+    result.corruptionQuarantined = true;
+    result.pendingDirty = true;
+}
 function readState(statePath) {
     try {
         return JSON.parse(fs.readFileSync(statePath, "utf8"));

package/dist/qmd-reindex.js.map

@@ -1 +1 @@
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package/dist/qmd-reindex.test.d.ts

@@ -5,6 +5,10 @@
  * fake `exec` that records the calls and returns canned results — no real qmd
  * is invoked. We assert on the *sequence of qmd commands* the function would
  * run, which is the contract that keeps a teammate's index fresh after sync.
+ *
+ * The corruption-safety tests (lock serialization, timeout-kill handling, and
+ * SQLITE_CORRUPT quarantine) pin the fix for feedback_b9a369ff — the post-sync
+ * reindex racing an interactive qmd writer and corrupting the vector store.
  */
 export {};
 //# sourceMappingURL=qmd-reindex.test.d.ts.map

package/dist/qmd-reindex.test.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"qmd-reindex.test.d.ts","sourceRoot":"","sources":["../src/qmd-reindex.test.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG"}
+{"version":3,"file":"qmd-reindex.test.d.ts","sourceRoot":"","sources":["../src/qmd-reindex.test.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG"}