akm-cli 0.9.0-beta.2 → 0.9.0-beta.4

package/dist/commands/remember.js

@@ -149,6 +149,10 @@ export async function runLlmEnrich(body) {
         return { tags: [] };
     }
     const { chatCompletion, parseEmbeddedJsonResponse: parseJsonResponse } = await import("../llm/client.js");
+    // #576: attribute this entry point's LLM call to the `remember` stage. The
+    // wrapper is ambient — if a usage sink is active it tags the record; if not,
+    // it is a no-op.
+    const { withLlmStage } = await import("../llm/usage-telemetry.js");
     const prompt = `You are a memory tagger for a developer knowledge base.
 Given the memory text below, return ONLY a JSON object with these fields:
 - "tags": array of 1-5 short lowercase keyword tags
@@ -164,10 +168,10 @@ Return ONLY the JSON object, no prose, no markdown fences.`;
         const result = await (async () => {
             try {
                 return await Promise.race([
-                    chatCompletion(llmConfig, [
+                    withLlmStage("remember", () => chatCompletion(llmConfig, [
                         { role: "system", content: "Return only valid JSON. No prose." },
                         { role: "user", content: prompt },
-                    ], { maxTokens: 256, temperature: 0.1 }),
+                    ], { maxTokens: 256, temperature: 0.1 })),
                     new Promise((_, reject) => {
                         timeoutHandle = setTimeout(() => reject(new Error("LLM enrichment timed out")), LLM_ENRICH_TIMEOUT_MS);
                     }),

package/dist/core/config/config-schema.js

@@ -138,6 +138,11 @@ export const ImproveProcessConfigSchema = z
     // Extract process config (only meaningful for extract process)
     defaultSince: z.string().min(1).optional(),
     maxTotalChars: positiveInt.optional(),
+    // Extract process: minimum raw session size (pre-filter inputCount) below
+    // which the extract LLM call is skipped (#595/#596). 0 disables the gate.
+    // Absent = default 10 (skip only truly empty sessions). Only meaningful
+    // on the `extract` process.
+    minContentChars: z.number().int().min(0).optional(),
     maxChunkSize: z.number().int().min(1).max(50).optional(),
     // Extract process: minimum number of new (unseen, in-window) candidate
     // sessions below which the extract pass skips entirely (emits an

package/dist/core/logs-db.js

@@ -0,0 +1,304 @@
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at https://mozilla.org/MPL/2.0/.
+/**
+ * logs.db — Dedicated SQLite database for task/run log lines (#579).
+ *
+ * Replaces grep-the-flat-file consumption of `<cacheDir>/tasks/logs/<id>/<ts>.log`
+ * with structured, indexed rows: `{ts, task_id, run_id, stream, level, line}`.
+ * The strategic direction (stop scattering data across files/folders) means
+ * every NEW log consumer queries this database; the per-run text file written
+ * by the task runner is retained only as a transitional tail for humans —
+ * see docs/technical/logs-audit.md for the full producer audit.
+ *
+ * ## Why a separate database from state.db
+ *
+ * Log lines are high-volume, append-only, and freely purgeable; state.db rows
+ * (events, proposals, task_history) are durable records. Separating them keeps
+ * state.db small and lets log retention be aggressive without touching durable
+ * state. Cross-db queries (e.g. "failed task_history row → its log lines") use
+ * SQLite ATTACH — see {@link attachStateDatabase}.
+ *
+ * ## run_id
+ *
+ * state.db's `task_history` identifies a run by the unique pair
+ * `(task_id, started_at)` (see migration 002 in state-db.ts). logs.db encodes
+ * that pair as a single string — {@link buildTaskRunId} — so log rows can be
+ * joined back to their history row:
+ *
+ *   l.run_id = th.task_id || '@' || th.started_at
+ *
+ * ## Schema evolution
+ *
+ * Same migration-safety contract as state.db: append-only `MIGRATIONS` applied
+ * through the shared runner in src/storage/engines/sqlite-migrations.ts.
+ *
+ * @module logs-db
+ */
+import fs from "node:fs";
+import path from "node:path";
+import { openDatabase } from "../storage/database.js";
+import { runMigrations as runSqliteMigrations } from "../storage/engines/sqlite-migrations.js";
+import { getDataDir } from "./paths.js";
+import { getStateDbPath } from "./state-db.js";
+// ── Path helper ──────────────────────────────────────────────────────────────
+/**
+ * Default path: `<dataDir>/logs.db` — alongside state.db so cooperating
+ * processes sharing a data root automatically share the same logs database
+ * (same `AKM_DATA_DIR` / XDG env-isolation as {@link getStateDbPath}).
+ */
+export function getLogsDbPath() {
+    return path.join(getDataDir(), "logs.db");
+}
+// ── Database open ────────────────────────────────────────────────────────────
+/**
+ * Open (and initialise / migrate) the logs database.
+ *
+ * @param dbPath - Override the database file path (tests pass a tmpdir path).
+ *
+ * PRAGMA rationale:
+ *
+ *   journal_mode = WAL
+ *     Readers never block writers and vice-versa; crashes are safe (the WAL is
+ *     replayed on next open). Required because the task runner writes log rows
+ *     while `akm health` may be reading them.
+ *
+ *   busy_timeout = 30000
+ *     Log writes happen at the end of scheduled task runs, which can pile up
+ *     (cron fan-out). 30 s of retry absorbs a slow concurrent writer instead of
+ *     surfacing SQLITE_BUSY and dropping log lines.
+ */
+export function openLogsDatabase(dbPath) {
+    const resolvedPath = dbPath ?? getLogsDbPath();
+    const dir = path.dirname(resolvedPath);
+    if (!fs.existsSync(dir)) {
+        fs.mkdirSync(dir, { recursive: true });
+    }
+    const db = openDatabase(resolvedPath);
+    // PRAGMAs must run before any DDL or DML.
+    db.exec("PRAGMA journal_mode = WAL");
+    db.exec("PRAGMA busy_timeout = 30000");
+    runMigrations(db);
+    return db;
+}
+// ── Migrations ───────────────────────────────────────────────────────────────
+/**
+ * All migrations in application order. APPEND only — never insert in the
+ * middle or reorder. Same contract as state.db's MIGRATIONS array.
+ */
+const MIGRATIONS = [
+    // ── Migration 001 — task_logs ───────────────────────────────────────────────
+    //
+    // One row per log line emitted by a task run.
+    //
+    // Indexed (query) columns:
+    //   ts       TEXT — ISO-8601 UTC; range queries ("logs in the last hour").
+    //   task_id  TEXT — task identifier; per-task log views.
+    //   run_id   TEXT — buildTaskRunId(task_id, started_at); per-run log views
+    //                   and the join key back to state.db task_history.
+    //
+    // Non-indexed columns:
+    //   stream   TEXT — 'stdout' | 'stderr'; which pipe the line came from.
+    //   level    TEXT — 'info' | 'warn' | 'error'; runner-assigned severity
+    //                   ('info' for captured stdout, 'error' for stderr and
+    //                   failure diagnostics).
+    //   line     TEXT — the log line itself (no trailing newline).
+    //
+    // ADD COLUMN extension points (future migrations):
+    //   ALTER TABLE task_logs ADD COLUMN seq INTEGER DEFAULT NULL;
+    //   ALTER TABLE task_logs ADD COLUMN source TEXT DEFAULT NULL;
+    //
+    // TTL: rows where ts < NOW() - retention can be deleted by purgeOldTaskLogs().
+    // No automatic deletion occurs here.
+    {
+        id: "001-task-logs",
+        up: `
+      CREATE TABLE IF NOT EXISTS task_logs (
+        id      INTEGER PRIMARY KEY AUTOINCREMENT,
+        ts      TEXT    NOT NULL,
+        task_id TEXT    NOT NULL,
+        run_id  TEXT    NOT NULL,
+        stream  TEXT    NOT NULL DEFAULT 'stdout',
+        level   TEXT    NOT NULL DEFAULT 'info',
+        line    TEXT    NOT NULL
+      );
+
+      -- Query patterns:
+      --   SELECT … WHERE ts >= ? AND ts <= ?   → idx_task_logs_ts (purge, windows)
+      --   SELECT … WHERE task_id = ?           → idx_task_logs_task_id
+      --   SELECT … WHERE run_id = ?            → idx_task_logs_run_id (per-run tail)
+      CREATE INDEX IF NOT EXISTS idx_task_logs_ts      ON task_logs(ts);
+      CREATE INDEX IF NOT EXISTS idx_task_logs_task_id ON task_logs(task_id);
+      CREATE INDEX IF NOT EXISTS idx_task_logs_run_id  ON task_logs(run_id);
+    `,
+    },
+];
+/**
+ * Apply every pending migration. Called automatically by
+ * {@link openLogsDatabase}; exported for the same test seams state-db exposes.
+ */
+export function runMigrations(db) {
+    runSqliteMigrations(db, MIGRATIONS);
+}
+// ── run_id ───────────────────────────────────────────────────────────────────
+/**
+ * Encode a task run's identity — the unique `(task_id, started_at)` pair from
+ * state.db `task_history` — as a single run_id string.
+ *
+ * The format MUST stay in sync with the SQL expression
+ * `task_id || '@' || started_at` used by {@link queryFailedRunLogLines}.
+ */
+export function buildTaskRunId(taskId, startedAtIso) {
+    return `${taskId}@${startedAtIso}`;
+}
+/**
+ * Insert a batch of log lines for one task run in a single transaction.
+ * Returns the number of rows inserted. Lines are stored in array order
+ * (ascending rowid), so reading back `ORDER BY id` reproduces emission order.
+ *
+ * Errors propagate — the task runner wraps this in its own best-effort
+ * handling (mirroring `appendHistory`) so an unwritable logs.db never fails
+ * a task run.
+ */
+export function insertTaskLogLines(db, input) {
+    if (input.lines.length === 0)
+        return 0;
+    const stmt = db.prepare(`INSERT INTO task_logs (ts, task_id, run_id, stream, level, line)
+     VALUES (?, ?, ?, ?, ?, ?)`);
+    db.transaction(() => {
+        for (const entry of input.lines) {
+            stmt.run(input.ts, input.taskId, input.runId, entry.stream ?? "stdout", entry.level ?? "info", entry.line);
+        }
+    })();
+    return input.lines.length;
+}
+/**
+ * Read log lines matching the filter, in emission order (ascending id).
+ *
+ * Connection-lifetime rule (WS5): `.all()` materializes a plain array before
+ * returning.
+ */
+export function queryTaskLogs(db, options = {}) {
+    const conditions = [];
+    const params = [];
+    if (options.taskId) {
+        conditions.push("task_id = ?");
+        params.push(options.taskId);
+    }
+    if (options.runId) {
+        conditions.push("run_id = ?");
+        params.push(options.runId);
+    }
+    if (options.stream) {
+        conditions.push("stream = ?");
+        params.push(options.stream);
+    }
+    if (options.since) {
+        conditions.push("ts >= ?");
+        params.push(options.since);
+    }
+    if (options.until) {
+        conditions.push("ts < ?");
+        params.push(options.until);
+    }
+    const where = conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "";
+    const limit = options.limit !== undefined && options.limit >= 0 ? ` LIMIT ${Math.floor(options.limit)}` : "";
+    return db
+        .prepare(`SELECT id, ts, task_id, run_id, stream, level, line FROM task_logs ${where} ORDER BY id ASC${limit}`)
+        .all(...params);
+}
+/**
+ * Bulk membership check: which of `runIds` have at least one log row?
+ * Used by `akm health` to compute the log-backing rate from the database
+ * instead of `fs.existsSync` over scattered files. Chunked to stay under
+ * SQLite's bound-parameter ceiling.
+ */
+export function getLoggedRunIds(db, runIds) {
+    const out = new Set();
+    if (runIds.length === 0)
+        return out;
+    const CHUNK = 500;
+    for (let i = 0; i < runIds.length; i += CHUNK) {
+        const chunk = runIds.slice(i, i + CHUNK);
+        const placeholders = chunk.map(() => "?").join(",");
+        const rows = db
+            .prepare(`SELECT DISTINCT run_id FROM task_logs WHERE run_id IN (${placeholders})`)
+            .all(...chunk);
+        for (const row of rows)
+            out.add(row.run_id);
+    }
+    return out;
+}
+// ── Cross-db: ATTACH state.db ────────────────────────────────────────────────
+/**
+ * ATTACH state.db to an open logs.db handle under the schema name `state`,
+ * enabling cross-db joins like task_history × task_logs.
+ *
+ * The state.db file must already exist (callers always open state.db first in
+ * practice); attaching a non-existent path would silently create an empty,
+ * unmigrated database file, so this throws instead.
+ */
+export function attachStateDatabase(db, stateDbPath) {
+    const resolved = stateDbPath ?? getStateDbPath();
+    if (!fs.existsSync(resolved)) {
+        throw new Error(`Cannot ATTACH state.db: file does not exist at ${resolved}`);
+    }
+    // prepare().run() rather than db.run(): both drivers support parameterised
+    // ATTACH through a prepared statement, and no other call site uses db.run().
+    db.prepare("ATTACH DATABASE ? AS state").run(resolved);
+}
+/**
+ * Convenience: open logs.db with state.db attached as `state`. The returned
+ * handle supports cross-db queries such as {@link queryFailedRunLogLines}.
+ * Close it like any other handle (DETACH is implicit on close).
+ */
+export function openLogsDatabaseWithState(logsDbPath, stateDbPath) {
+    const db = openLogsDatabase(logsDbPath);
+    try {
+        attachStateDatabase(db, stateDbPath);
+    }
+    catch (err) {
+        db.close();
+        throw err;
+    }
+    return db;
+}
+/**
+ * Cross-db join: every log line belonging to a FAILED task_history run whose
+ * `started_at` is `>= since` (all failed runs when omitted). Requires a handle
+ * opened via {@link openLogsDatabaseWithState}.
+ *
+ * The join key is the run_id encoding documented on {@link buildTaskRunId}:
+ * `task_logs.run_id = task_history.task_id || '@' || task_history.started_at`.
+ */
+export function queryFailedRunLogLines(db, options = {}) {
+    const conditions = ["th.status = 'failed'"];
+    const params = [];
+    if (options.since) {
+        conditions.push("th.started_at >= ?");
+        params.push(options.since);
+    }
+    const limit = options.limit !== undefined && options.limit >= 0 ? ` LIMIT ${Math.floor(options.limit)}` : "";
+    return db
+        .prepare(`SELECT th.task_id, l.run_id, th.started_at, th.status, l.ts, l.stream, l.level, l.line
+       FROM state.task_history th
+       JOIN task_logs l ON l.run_id = th.task_id || '@' || th.started_at
+       WHERE ${conditions.join(" AND ")}
+       ORDER BY th.started_at DESC, l.id ASC${limit}`)
+        .all(...params);
+}
+// ── Retention ────────────────────────────────────────────────────────────────
+/**
+ * Delete task_logs rows older than `retentionDays` (default: 90). Mirrors
+ * `purgeOldEvents` / `purgeOldImproveRuns` in state-db.ts — same default, same
+ * return shape (rows deleted), same disabled-when-non-positive semantics.
+ * Wired into the improve maintenance pass alongside the state.db purges.
+ */
+export function purgeOldTaskLogs(db, retentionDays = 90) {
+    if (!Number.isFinite(retentionDays) || retentionDays <= 0)
+        return 0;
+    const cutoff = new Date(Date.now() - retentionDays * 86_400_000).toISOString();
+    const result = db.prepare("DELETE FROM task_logs WHERE ts < ?").run(cutoff);
+    const changes = result.changes ?? 0;
+    return typeof changes === "bigint" ? Number(changes) : changes;
+}

package/dist/core/state-db.js

@@ -86,11 +86,12 @@ export function getStateDbPath() {
  *     backwards compatibility; enabling them prevents orphaned rows in tables
  *     that reference each other (not used in v1 schema but guards future ones).
  *
- *   busy_timeout = 5000
+ *   busy_timeout = 30000
  *     When another connection holds a write lock, SQLite retries for up to
- *     5 000 ms before returning SQLITE_BUSY. Without this, the default timeout
- *     is 0 ms — any concurrent writer causes an immediate error. 5 s matches
- *     the same value used in openDatabase() for index.db.
+ *     30 000 ms before returning SQLITE_BUSY. Without this, the default timeout
+ *     is 0 ms — any concurrent writer causes an immediate error. 30 s (#589)
+ *     matches the value used in openDatabase() for index.db; 5 s proved too
+ *     narrow when a post-inference reindex overlapped a parallel event write.
  */
 export function openStateDatabase(dbPath) {
     const resolvedPath = dbPath ?? getStateDbPath();
@@ -102,7 +103,7 @@ export function openStateDatabase(dbPath) {
     // PRAGMAs must run before any DDL or DML.
     db.exec("PRAGMA journal_mode = WAL");
     db.exec("PRAGMA foreign_keys = ON");
-    db.exec("PRAGMA busy_timeout = 5000");
+    db.exec("PRAGMA busy_timeout = 30000");
     runMigrations(db);
     return db;
 }
@@ -190,7 +191,9 @@ const MIGRATIONS = [
       --
       -- Extensible (metadata_json) columns:
       --   metadata_json TEXT      — JSON object for future proposal fields.
-      --                             Current fields stored here: sourceRun, review.
+      --                             Current fields stored here: sourceRun,
+      --                             review, confidence, gateDecision (#577),
+      --                             backupContent.
       --
       -- ADD COLUMN extension points (future migrations):
       --   ALTER TABLE proposals ADD COLUMN source_run TEXT DEFAULT NULL;
@@ -458,6 +461,33 @@ const MIGRATIONS = [
         ON extract_sessions_seen(processed_at);
     `,
     },
+    // ── Migration 005 — proposal_fs_imports ─────────────────────────────────────
+    //
+    // One-shot ledger for the legacy filesystem→SQLite proposal import (#578).
+    //
+    // Before 0.9.0 the proposal queue lived as per-uuid JSON directories under
+    // `<stashDir>/.akm/proposals/` and the `proposals` table (created in 001) was
+    // dead weight. 0.9.0 makes the table canonical; the first proposal operation
+    // against a stash imports any legacy `proposal.json` files it finds (INSERT
+    // OR IGNORE, so re-runs never duplicate) and records the stash here so later
+    // invocations skip the directory walk entirely.
+    //
+    // Indexed (query) columns:
+    //   stash_dir    TEXT PK  — absolute stash root the import ran against.
+    //
+    // Non-indexed columns:
+    //   imported_at    TEXT     — ISO-8601 UTC; when the import completed.
+    //   imported_count INTEGER  — rows actually inserted by the import.
+    {
+        id: "005-proposal-fs-imports",
+        up: `
+      CREATE TABLE IF NOT EXISTS proposal_fs_imports (
+        stash_dir      TEXT    PRIMARY KEY,
+        imported_at    TEXT    NOT NULL,
+        imported_count INTEGER NOT NULL DEFAULT 0
+      );
+    `,
+    },
 ];
 /**
  * Apply every pending migration in a single transaction per migration.
@@ -529,6 +559,9 @@ export function proposalRowToProposal(row) {
             ...(frontmatter !== undefined ? { frontmatter } : {}),
         },
         ...(meta.review !== undefined ? { review: meta.review } : {}),
+        ...(typeof meta.confidence === "number" ? { confidence: meta.confidence } : {}),
+        ...(meta.gateDecision !== undefined ? { gateDecision: meta.gateDecision } : {}),
+        ...(typeof meta.backupContent === "string" ? { backupContent: meta.backupContent } : {}),
     };
 }
 /**
@@ -542,6 +575,12 @@ export function proposalToRowValues(proposal, stashDir) {
         metaObj.sourceRun = proposal.sourceRun;
     if (proposal.review !== undefined)
         metaObj.review = proposal.review;
+    if (proposal.confidence !== undefined)
+        metaObj.confidence = proposal.confidence;
+    if (proposal.gateDecision !== undefined)
+        metaObj.gateDecision = proposal.gateDecision;
+    if (proposal.backupContent !== undefined)
+        metaObj.backupContent = proposal.backupContent;
     return {
         id: proposal.id,
         stash_dir: stashDir,
@@ -656,7 +695,10 @@ export function upsertProposal(db, proposal, stashDir) {
 }
 /**
  * List proposals, optionally filtered by stashDir, status, and/or ref.
- * Results are sorted by created_at ASC to match the existing listProposals() behaviour.
+ *
+ * Results are ordered by `created_at ASC` (matching the historical
+ * `listProposals()` sort), with `rowid` as a deterministic tiebreak so two
+ * proposals created in the same millisecond list in insertion order.
  */
 export function listStateProposals(db, options = {}) {
     const conditions = [];
@@ -677,21 +719,72 @@ export function listStateProposals(db, options = {}) {
     const rows = db
         .prepare(`SELECT id, stash_dir, ref, status, source, created_at, updated_at,
               content, frontmatter_json, metadata_json
-       FROM proposals ${where} ORDER BY created_at ASC`)
+       FROM proposals ${where} ORDER BY created_at ASC, rowid ASC`)
         .all(...params);
     return rows.map(proposalRowToProposal);
 }
 /**
- * Look up a single proposal by id. Returns undefined when not found.
+ * Look up a single proposal by id, optionally scoped to one stash root.
+ * Returns undefined when not found.
  */
-export function getStateProposal(db, id) {
-    const row = db
-        .prepare(`SELECT id, stash_dir, ref, status, source, created_at, updated_at,
+export function getStateProposal(db, id, stashDir) {
+    const sql = `SELECT id, stash_dir, ref, status, source, created_at, updated_at,
               content, frontmatter_json, metadata_json
-       FROM proposals WHERE id = ?`)
-        .get(id);
+       FROM proposals WHERE id = ?${stashDir ? " AND stash_dir = ?" : ""}`;
+    const row = (stashDir ? db.prepare(sql).get(id, stashDir) : db.prepare(sql).get(id));
     return row ? proposalRowToProposal(row) : undefined;
 }
+/**
+ * Find PENDING proposal ids in one stash whose id starts with `idPrefix`.
+ * Backs the UUID-prefix form of `akm proposal show/accept/... <prefix>` —
+ * prefix resolution is deliberately scoped to the live (pending) queue,
+ * mirroring the historical behaviour of scanning only the live directory.
+ *
+ * `%` / `_` / `\` in the prefix are escaped so the LIKE pattern is literal.
+ */
+export function listStateProposalIdsByPrefix(db, stashDir, idPrefix) {
+    const escaped = idPrefix.replace(/[\\%_]/g, (ch) => `\\${ch}`);
+    const rows = db
+        .prepare(`SELECT id FROM proposals
+       WHERE stash_dir = ? AND status = 'pending' AND id LIKE ? ESCAPE '\\'
+       ORDER BY id ASC`)
+        .all(stashDir, `${escaped}%`);
+    return rows.map((r) => r.id);
+}
+/**
+ * Whether the legacy filesystem proposal import has already run for `stashDir`.
+ * See migration 005 (`proposal_fs_imports`).
+ */
+export function hasImportedFsProposals(db, stashDir) {
+    // Drivers disagree on the no-row sentinel (bun:sqlite → null,
+    // better-sqlite3 → undefined) — Boolean() covers both.
+    return Boolean(db.prepare("SELECT 1 FROM proposal_fs_imports WHERE stash_dir = ?").get(stashDir));
+}
+/**
+ * Record that the legacy filesystem proposal import completed for `stashDir`
+ * so subsequent invocations skip the directory walk. INSERT OR REPLACE keeps
+ * the call idempotent.
+ */
+export function recordFsProposalsImport(db, stashDir, importedCount) {
+    db.prepare("INSERT OR REPLACE INTO proposal_fs_imports (stash_dir, imported_at, imported_count) VALUES (?, ?, ?)").run(stashDir, new Date().toISOString(), importedCount);
+}
+/**
+ * Insert a proposal row ONLY when the id is not already present (used by the
+ * legacy filesystem import so re-runs never clobber rows that have since been
+ * mutated through the canonical store). Returns true when a row was inserted.
+ */
+export function insertProposalIfAbsent(db, proposal, stashDir) {
+    const v = proposalToRowValues(proposal, stashDir);
+    const result = db
+        .prepare(`
+      INSERT OR IGNORE INTO proposals
+        (id, stash_dir, ref, status, source, created_at, updated_at, content, frontmatter_json, metadata_json)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `)
+        .run(v.id, v.stash_dir, v.ref, v.status, v.source, v.created_at, v.updated_at, v.content, v.frontmatter_json, v.metadata_json);
+    const changes = result.changes ?? 0;
+    return Number(changes) > 0;
+}
 // ── task_history table helpers ───────────────────────────────────────────────
 /**
  * Upsert a task history row.

package/dist/indexer/db/db.js

@@ -28,7 +28,7 @@ export function openDatabase(dbPath, options) {
     }
     const db = openSqlite(resolvedPath);
     db.exec("PRAGMA journal_mode = WAL");
-    db.exec("PRAGMA busy_timeout = 5000");
+    db.exec("PRAGMA busy_timeout = 30000");
     db.exec("PRAGMA foreign_keys = ON");
     // Try to load sqlite-vec extension
     loadVecExtension(db);
@@ -69,7 +69,7 @@ export function openExistingDatabase(dbPath) {
     const resolvedPath = dbPath ?? getDbPath();
     const db = openSqlite(resolvedPath);
     db.exec("PRAGMA journal_mode = WAL");
-    db.exec("PRAGMA busy_timeout = 5000");
+    db.exec("PRAGMA busy_timeout = 30000");
     db.exec("PRAGMA foreign_keys = ON");
     // Existing-DB callers must not mutate schema or embedding metadata on open,
     // but some paths still need write access to usage_events and other tables.

package/dist/indexer/passes/memory-inference.js

@@ -119,6 +119,26 @@ export async function runMemoryInferencePass(ctx) {
         // 2026-05-26).
         if (signal?.aborted)
             return { aborted: true };
+        // Pre-check (#588): when `<parent>.derived.md` is already on disk the
+        // inference is by definition complete — the parent only looks pending
+        // because `markParentProcessed` never ran (process killed between the
+        // child write and the mark) or the child was created externally (e.g.
+        // consolidation). Skip the LLM/cache call entirely and mark the parent
+        // so it never re-pends. Before this check, production measurements
+        // showed ~55% of the pass's LLM budget re-deriving such parents only to
+        // discover the existing child after the fact.
+        if (fs.existsSync(derivedChildPath(record))) {
+            markParentProcessed(record);
+            return {
+                skipped: false,
+                splitParent: false,
+                written: 0,
+                fromCache: false,
+                retryAttempts: 0,
+                childExists: true,
+                precheck: true,
+            };
+        }
         // Incremental cache: skip LLM call when body hash is unchanged and
         // --re-enrich was not requested. The cache ref is the absolute file path.
         const validate = (raw) => {
@@ -171,23 +191,30 @@ export async function runMemoryInferencePass(ctx) {
             return { skipped: false, splitParent: true, written: writeOutcome.written, fromCache, retryAttempts };
         }
         // LLM produced a valid derived draft but no file was written — either
-        // because `<parent>.derived.md` already exists on disk or
-        // `writeAssetToSource` threw. Categorise as `childExists` so the
-        // attempt is accounted for in health metrics rather than vanishing
-        // into the freshAttempts denominator.
+        // because `<parent>.derived.md` appeared on disk after the pre-check
+        // above (a rare mid-flight race) or `writeAssetToSource` threw.
+        // Categorise as `childExists` so the consumed attempt is accounted for
+        // in health metrics rather than vanishing into the freshAttempts
+        // denominator.
         //
-        // When the child already exists on disk the inference is, by definition,
-        // already complete — so mark the parent processed here too (#550).
-        // Without this, `isPendingMemory()` re-queues the same parent every run
-        // (the `written > 0` path was previously the only site that marks it),
-        // causing permanent re-queueing and wasted LLM calls. A genuine write
-        // *failure* (`writeAssetToSource` threw) must NOT mark the parent — it
-        // should be retried next run — so we key off the explicit `childExists`
-        // outcome rather than the conflated `written === 0`.
+        // When the child exists the inference is, by definition, complete — so
+        // mark the parent processed here too (#550), otherwise
+        // `isPendingMemory()` re-queues the same parent every run. A genuine
+        // write *failure* (`writeAssetToSource` threw) must NOT mark the parent
+        // — it should be retried next run — so we key off the explicit
+        // `childExists` outcome rather than the conflated `written === 0`.
         if (writeOutcome.childExists) {
             markParentProcessed(record);
         }
-        return { skipped: false, splitParent: false, written: 0, fromCache, retryAttempts, childExists: true };
+        return {
+            skipped: false,
+            splitParent: false,
+            written: 0,
+            fromCache,
+            retryAttempts,
+            childExists: true,
+            precheck: false,
+        };
     }, 
     // Default concurrency of 4 for cloud APIs. Set `llm.concurrency: 1`
     // in config.json for local model servers (LM Studio, Ollama).
@@ -224,11 +251,16 @@ export async function runMemoryInferencePass(ctx) {
             result.writtenFacts += res.written;
         }
         else if ("childExists" in res && res.childExists) {
-            // LLM call was consumed but the derived file already existed (or the
-            // write threw). Track separately so this category is observable in
-            // health output and stops bleeding into the freshAttempts denominator.
+            // Derived child already on disk. Track separately so this category is
+            // observable in health output and stops bleeding into the
+            // freshAttempts denominator. Pre-check skips (#588) are the routine
+            // self-healing path — no LLM attempt was consumed and the parent has
+            // been marked processed — so only the rare post-LLM case (mid-flight
+            // race or write failure) warrants a per-ref warning.
             result.skippedChildExists += 1;
-            warn(`memory inference: derived child for ${pending[i]?.ref ?? "<unknown>"} already existed or write failed; counted as skippedChildExists`);
+            if (!res.precheck) {
+                warn(`memory inference: derived child for ${pending[i]?.ref ?? "<unknown>"} already existed or write failed; counted as skippedChildExists`);
+            }
         }
         else {
             // The per-record state machine should cover every outcome. A hit here
@@ -324,6 +356,14 @@ function toMemoryName(memoriesDir, filePath) {
     // user has organised under memories/.
     return rel.replace(/\\/g, "/").replace(/\.md$/i, "");
 }
+/**
+ * Absolute path of the derived child for a parent memory. Single source of
+ * truth for the `<parent>.derived.md` naming convention — used both by the
+ * pre-LLM existence check (#588) and the write path.
+ */
+function derivedChildPath(parent) {
+    return path.join(parent.stashRoot, "memories", `${parent.name}.derived.md`);
+}
 async function writeDerivedMemory(parent, derived) {
     const writeTarget = {
         kind: "filesystem",
@@ -338,11 +378,10 @@ async function writeDerivedMemory(parent, derived) {
     };
     const childName = `${parent.name}.derived`;
     const childRefStr = `memory:${childName}`;
-    const childPath = path.join(parent.stashRoot, "memories", `${childName}.md`);
-    if (fs.existsSync(childPath)) {
-        // The derived child is already on disk — inference for this parent is
-        // complete. Report `childExists` so the caller marks the parent processed
-        // (#550) instead of re-queueing it forever.
+    if (fs.existsSync(derivedChildPath(parent))) {
+        // The derived child appeared on disk after the caller's pre-check (#588)
+        // — a rare mid-flight race. Report `childExists` so the caller marks the
+        // parent processed (#550) instead of re-queueing it forever.
         return { written: 0, childExists: true };
     }
     try {