@cleocode/core 2026.10.21 → 2026.10.22

package/dist/memory/auto-row-quarantine.d.ts.map

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package/dist/memory/auto-row-quarantine.js

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+/**
+ * Reversible quarantine of auto-generated BRAIN rows (T13951, owner decision
+ * D11179).
+ *
+ * Three kinds of rows were written by machinery, not by anyone recording
+ * knowledge: dispatch traces (`brain_patterns`, one per agent resolution until
+ * T13946), "Doc attached" records (`brain_observations`, until T13985) and the
+ * content-free task-start/complete stubs. Recall already ignores them
+ * (`eligibility.ts#autoRowExclusionClause`); this module retires them from the
+ * active store by setting `invalid_at` only. Nothing is deleted.
+ *
+ * Safety contract (lead conditions on D11179):
+ * - Dry run by default: per-store, per-table counts and the exact predicates.
+ * - Apply refuses unless the caller passes the counts of a dry run taken in the
+ *   same state, so it never touches more rows than were approved.
+ * - The receipt (ids per store and table, timestamp, predicates, counts) is
+ *   written durably BEFORE the first write, so a crash mid-apply leaves a
+ *   receipt restore can use.
+ * - Restore clears `invalid_at` only where it still equals the receipt's
+ *   timestamp, so it is idempotent and never undoes a later invalidation.
+ * - Writes go through the canonical accessors, in batches, and sync.
+ *
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ *
+ * @module memory/auto-row-quarantine
+ * @task T13951
+ */
+import { createHash } from 'node:crypto';
+import { closeSync, fsyncSync, mkdirSync, openSync, readFileSync, renameSync, writeSync, } from 'node:fs';
+import { dirname, join } from 'node:path';
+import { z } from 'zod';
+import { AUTO_ROW_RULES, CURRENT_UNVERIFIED, } from './auto-row-rules.js';
+/** Brain stores the quarantine covers, reported separately. */
+export const QUARANTINE_SCOPES = ['project', 'global'];
+/** Memory tables holding auto rows. */
+export const QUARANTINE_TABLES = ['patterns', 'observations'];
+/** Build one value per store. */
+function perScope(make) {
+    return { project: make('project'), global: make('global') };
+}
+/** An all-zero tally. */
+function zeroTally() {
+    return perScope(() => ({ patterns: 0, observations: 0 }));
+}
+/** Default rows per write transaction. */
+export const QUARANTINE_BATCH_SIZE = 500;
+/** Error with a stable code for the CLI envelope. */
+export class AutoRowQuarantineError extends Error {
+    code;
+    /**
+     * @param code - Stable error code.
+     * @param message - Human-readable explanation.
+     */
+    constructor(code, message) {
+        super(message);
+        this.code = code;
+        this.name = 'AutoRowQuarantineError';
+    }
+}
+/**
+ * Open the project and global brain stores with accessor-backed writers.
+ *
+ * @param projectRoot - Project whose brain is the `project` store.
+ * @returns Read handles and writers for both stores.
+ * @example
+ * ```ts
+ * const stores = await openQuarantineStores(projectRoot);
+ * ```
+ */
+export async function openQuarantineStores(projectRoot) {
+    const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
+    const { getBrainAccessor, setGlobalInvalidAtWhere } = await import('../store/memory-accessor.js');
+    const { getDualScopeNativeDb, openDualScopeDb } = await import('../store/dual-scope-db.js');
+    await getBrainDb(projectRoot);
+    const projectDb = getBrainNativeDb(projectRoot);
+    // @sync-invariant none:local-only no store handle, so nothing is read or written
+    if (!projectDb)
+        throw new Error('BRAIN database unavailable for the auto-row quarantine');
+    const accessor = await getBrainAccessor(projectRoot);
+    return {
+        project: { db: projectDb, write: (...args) => accessor.setInvalidAtWhere(...args) },
+        global: {
+            db: getDualScopeNativeDb(await openDualScopeDb('global')),
+            write: setGlobalInvalidAtWhere,
+        },
+    };
+}
+/**
+ * Dry run: what an apply would quarantine in each store, with the predicates.
+ *
+ * @param stores - Project and global stores.
+ * @returns Counts, predicates and ids. Nothing is written.
+ * @example
+ * ```ts
+ * const plan = planAutoRowQuarantine(await openQuarantineStores(root));
+ * ```
+ */
+export function planAutoRowQuarantine(stores) {
+    const ids = perScope((scope) => idsFor(stores[scope].db));
+    return {
+        counts: perScope((scope) => countsFor(stores[scope].db, ids[scope])),
+        predicates: Object.fromEntries(AUTO_ROW_RULES.map((rule) => [rule.id, `${rule.predicate} AND ${CURRENT_UNVERIFIED}`])),
+        ids,
+        digest: digestIds(ids),
+    };
+}
+/**
+ * Short, stable digest of an id set (sha256 of the sorted ids per store and
+ * table, first 16 hex characters). Approval binds to it, so an apply cannot
+ * quarantine a different set of rows with the same counts.
+ *
+ * @param ids - Ids per store and table.
+ * @returns 16 hex characters.
+ * @example
+ * ```ts
+ * digestIds(plan.ids); // '3f2a9c0d1b7e4a55'
+ * ```
+ */
+export function digestIds(ids) {
+    const canonical = QUARANTINE_SCOPES.flatMap((scope) => QUARANTINE_TABLES.map((table) => [scope, table, [...ids[scope][table]].sort()]));
+    return createHash('sha256').update(JSON.stringify(canonical)).digest('hex').slice(0, 16);
+}
+/** The rules a table's rows must still match when a batch writes them. */
+function tableRules(table) {
+    return AUTO_ROW_RULES.filter((rule) => rule.table === table).map((rule) => rule.id);
+}
+/** Ids one rule matches in one store. */
+function ruleIds(db, rule) {
+    return db
+        .prepare(`SELECT id FROM main.brain_${rule.table}
+       WHERE (${rule.predicate}) AND ${CURRENT_UNVERIFIED} ORDER BY id`)
+        .all()
+        .map((row) => String(row.id));
+}
+/** Distinct matching ids per table for one store. */
+function idsFor(db) {
+    const ids = (table) => [
+        ...new Set(AUTO_ROW_RULES.filter((rule) => rule.table === table).flatMap((rule) => ruleIds(db, rule))),
+    ].sort();
+    return { patterns: ids('patterns'), observations: ids('observations') };
+}
+/** Per-table and per-rule counts for one store. */
+function countsFor(db, ids) {
+    const byRule = (table) => Object.fromEntries(AUTO_ROW_RULES.filter((rule) => rule.table === table).map((rule) => [
+        rule.id,
+        ruleIds(db, rule).length,
+    ]));
+    return {
+        patterns: { count: ids.patterns.length, byRule: byRule('patterns') },
+        observations: { count: ids.observations.length, byRule: byRule('observations') },
+    };
+}
+/**
+ * Parse `--expect` counts: `project:patterns=N,project:observations=N,global:...`.
+ * Every store/table pair must be given, once.
+ *
+ * @param text - The flag value.
+ * @returns Expected counts per store and table.
+ * @throws AutoRowQuarantineError when a pair is missing, repeated or malformed.
+ * @example
+ * ```ts
+ * parseQuarantineExpect('project:patterns=3,project:observations=1,global:patterns=0,global:observations=0');
+ * ```
+ */
+export function parseQuarantineExpect(text) {
+    const given = new Map();
+    for (const part of text.split(',')) {
+        const match = /^\s*(project|global):(patterns|observations)=(\d+)\s*$/.exec(part);
+        if (!match) {
+            throw new AutoRowQuarantineError('E_QUARANTINE_EXPECT_MISMATCH', `Malformed --expect entry '${part}'; use <project|global>:<patterns|observations>=<count>`);
+        }
+        const pair = `${match[1]}:${match[2]}`;
+        if (given.has(pair)) {
+            // @sync-invariant none:input-shape a doubled --expect pair is refused before any write
+            throw new AutoRowQuarantineError('E_QUARANTINE_EXPECT_MISMATCH', `--expect gives ${pair} more than once; pass each count once`);
+        }
+        given.set(pair, Number(match[3]));
+    }
+    const count = (scope, table) => {
+        const value = given.get(`${scope}:${table}`);
+        if (value === undefined) {
+            throw new AutoRowQuarantineError('E_QUARANTINE_EXPECT_MISMATCH', `--expect must give ${scope}:${table}; pass every count from the dry run`);
+        }
+        return value;
+    };
+    return perScope((scope) => ({
+        patterns: count(scope, 'patterns'),
+        observations: count(scope, 'observations'),
+    }));
+}
+/** Write JSON durably: temp file, fsync, rename. */
+function writeDurably(path, value) {
+    mkdirSync(dirname(path), { recursive: true });
+    const temp = `${path}.tmp`;
+    const fd = openSync(temp, 'w');
+    try {
+        writeSync(fd, `${JSON.stringify(value, null, 2)}\n`);
+        fsyncSync(fd);
+    }
+    finally {
+        closeSync(fd);
+    }
+    renameSync(temp, path);
+    // Best effort: make the rename itself durable (not supported on every platform).
+    try {
+        const dirFd = openSync(dirname(path), 'r');
+        try {
+            fsyncSync(dirFd);
+        }
+        finally {
+            closeSync(dirFd);
+        }
+    }
+    catch {
+        // A directory fsync is unavailable here; the receipt file itself is synced.
+    }
+}
+/**
+ * Default receipt path for an apply at `quarantinedAt` (gitignored backups).
+ *
+ * @param projectRoot - Project root.
+ * @param quarantinedAt - ISO timestamp of the apply.
+ * @returns Absolute receipt path.
+ * @example
+ * ```ts
+ * defaultQuarantineReceiptPath(root, '2026-10-24T00:00:00.000Z');
+ * ```
+ */
+export function defaultQuarantineReceiptPath(projectRoot, quarantinedAt) {
+    return join(projectRoot, '.cleo', 'backups', 'quarantine', `auto-rows-${quarantinedAt.replace(/[:.]/g, '-')}.json`);
+}
+/**
+ * Apply the quarantine after checking the approved counts still hold.
+ *
+ * @param stores - Project and global stores.
+ * @param expect - Counts from the approved dry run; any difference refuses.
+ * @param expectDigest - Id-set digest from the approved dry run; any difference refuses.
+ * @param receiptPath - Where the receipt is written (before the first write).
+ * @param options - `batchSize` per write transaction; `now` for tests.
+ * @returns The completed receipt.
+ * @throws AutoRowQuarantineError when the current counts differ from `expect`.
+ * @example
+ * ```ts
+ * const receipt = await applyAutoRowQuarantine(stores, expect, path);
+ * ```
+ */
+export async function applyAutoRowQuarantine(stores, expect, expectDigest, receiptPath, options = {}) {
+    const plan = planAutoRowQuarantine(stores);
+    if (plan.digest !== expectDigest) {
+        // @sync-invariant none:input-shape the approved row set no longer holds; nothing is written
+        throw new AutoRowQuarantineError('E_QUARANTINE_EXPECT_MISMATCH', `The matched rows now digest to ${plan.digest}, not the approved ${expectDigest}; run the dry run again`);
+    }
+    for (const scope of QUARANTINE_SCOPES) {
+        for (const table of QUARANTINE_TABLES) {
+            if (plan.counts[scope][table].count !== expect[scope][table]) {
+                // @sync-invariant none:input-shape the approved counts no longer hold; nothing is written
+                throw new AutoRowQuarantineError('E_QUARANTINE_EXPECT_MISMATCH', `${scope}:${table} now matches ${plan.counts[scope][table].count} rows, not the approved ${expect[scope][table]}; run the dry run again`);
+            }
+        }
+    }
+    const receipt = {
+        version: 1,
+        quarantinedAt: (options.now ?? new Date()).toISOString(),
+        status: 'started',
+        predicates: plan.predicates,
+        counts: expect,
+        ids: plan.ids,
+        digest: plan.digest,
+    };
+    writeDurably(receiptPath, receipt);
+    const batchSize = options.batchSize ?? QUARANTINE_BATCH_SIZE;
+    const quarantined = zeroTally();
+    const skipped = perScope(() => ({ patterns: [], observations: [] }));
+    for (const scope of QUARANTINE_SCOPES) {
+        for (const table of QUARANTINE_TABLES) {
+            const ids = plan.ids[scope][table];
+            for (let start = 0; start < ids.length; start += batchSize) {
+                const batch = ids.slice(start, start + batchSize);
+                // Re-check the full predicate: a row verified or edited mid-apply is skipped.
+                const changed = new Set(await stores[scope].write(table, batch, receipt.quarantinedAt, null, tableRules(table)));
+                quarantined[scope][table] += changed.size;
+                skipped[scope][table].push(...batch.filter((id) => !changed.has(id)));
+            }
+        }
+    }
+    const complete = {
+        ...receipt,
+        status: 'complete',
+        quarantined,
+        skipped,
+    };
+    writeDurably(receiptPath, complete);
+    return complete;
+}
+/**
+ * Restore a quarantine from its receipt: clear `invalid_at` on the listed rows
+ * that still carry the receipt's timestamp. Idempotent; works on a receipt left
+ * `started` by an interrupted apply.
+ *
+ * @param stores - Project and global stores.
+ * @param receiptPath - The receipt an apply wrote.
+ * @param options - `batchSize` per write transaction.
+ * @returns Rows restored per store and table.
+ * @throws AutoRowQuarantineError when the receipt is unreadable or malformed.
+ * @example
+ * ```ts
+ * const restored = await restoreAutoRowQuarantine(stores, path);
+ * ```
+ */
+export async function restoreAutoRowQuarantine(stores, receiptPath, options = {}) {
+    const receipt = readReceipt(receiptPath);
+    const batchSize = options.batchSize ?? QUARANTINE_BATCH_SIZE;
+    const restored = zeroTally();
+    for (const scope of QUARANTINE_SCOPES) {
+        for (const table of QUARANTINE_TABLES) {
+            const ids = receipt.ids[scope][table];
+            for (let start = 0; start < ids.length; start += batchSize) {
+                const changed = await stores[scope].write(table, ids.slice(start, start + batchSize), null, receipt.quarantinedAt);
+                restored[scope][table] += changed.length;
+            }
+        }
+    }
+    return restored;
+}
+const tallySchema = z.object({ patterns: z.number(), observations: z.number() });
+const idsSchema = z.object({ patterns: z.array(z.string()), observations: z.array(z.string()) });
+const receiptSchema = z.object({
+    version: z.literal(1),
+    quarantinedAt: z.string().min(1),
+    status: z.enum(['started', 'complete']),
+    predicates: z.record(z.string(), z.string()),
+    counts: z.object({ project: tallySchema, global: tallySchema }),
+    ids: z.object({ project: idsSchema, global: idsSchema }),
+    digest: z.string(),
+    quarantined: z.object({ project: tallySchema, global: tallySchema }).optional(),
+    skipped: z.object({ project: idsSchema, global: idsSchema }).optional(),
+});
+/** Read and validate a receipt. */
+function readReceipt(path) {
+    let text;
+    try {
+        text = readFileSync(path, 'utf8');
+    }
+    catch (err) {
+        // @sync-invariant none:input-shape an unreadable receipt is refused before any write
+        throw new AutoRowQuarantineError('E_QUARANTINE_RECEIPT', `Cannot read quarantine receipt ${path}: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    let json;
+    try {
+        json = JSON.parse(text);
+    }
+    catch {
+        // @sync-invariant none:input-shape an unparseable receipt is refused before any write
+        throw new AutoRowQuarantineError('E_QUARANTINE_RECEIPT', `Receipt ${path} is not valid JSON`);
+    }
+    const parsed = receiptSchema.safeParse(json);
+    if (!parsed.success) {
+        // @sync-invariant none:input-shape a malformed receipt is refused before any write
+        throw new AutoRowQuarantineError('E_QUARANTINE_RECEIPT', `Not a quarantine receipt: ${path}`);
+    }
+    return parsed.data;
+}
+//# sourceMappingURL=auto-row-quarantine.js.map

package/dist/memory/auto-row-quarantine.js.map

@@ -0,0 +1 @@
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package/dist/memory/auto-row-rules.d.ts

@@ -0,0 +1,29 @@
+/** Stable id of an auto-row rule. */
+export type AutoRowRuleId = 'dispatch-trace' | 'doc-attachment' | 'task-stub';
+/** One named auto-row rule with its exact SQL predicate. */
+export interface AutoRowRule {
+    /** Stable id, reported in counts. */
+    readonly id: AutoRowRuleId;
+    /** Table the rule reads. */
+    readonly table: 'patterns' | 'observations';
+    /** SQL predicate over unaliased columns, ANDed with the current/unverified guard. */
+    readonly predicate: string;
+}
+/** Guard every rule shares: only current, unverified rows. */
+export declare const CURRENT_UNVERIFIED = "invalid_at IS NULL AND COALESCE(verified, 0) != 1";
+/** The rules, each matching rows only machinery writes. */
+export declare const AUTO_ROW_RULES: readonly AutoRowRule[];
+/**
+ * The SQL guard for a write: any of the named rules, on current unverified rows.
+ *
+ * @param table - Table being written.
+ * @param ruleIds - Rules the row must still match.
+ * @returns A predicate over unaliased columns.
+ * @throws Error when no rule is named, or a rule is unknown or reads another table.
+ * @example
+ * ```ts
+ * const guard = autoRowGuard('patterns', ['dispatch-trace']);
+ * ```
+ */
+export declare function autoRowGuard(table: 'patterns' | 'observations', ruleIds: readonly AutoRowRuleId[]): string;
+//# sourceMappingURL=auto-row-rules.d.ts.map

package/dist/memory/auto-row-rules.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"auto-row-rules.d.ts","sourceRoot":"","sources":["../../src/memory/auto-row-rules.ts"],"names":[],"mappings":"AAQA,qCAAqC;AACrC,MAAM,MAAM,aAAa,GAAG,gBAAgB,GAAG,gBAAgB,GAAG,WAAW,CAAC;AAE9E,4DAA4D;AAC5D,MAAM,WAAW,WAAW;IAC1B,qCAAqC;IACrC,QAAQ,CAAC,EAAE,EAAE,aAAa,CAAC;IAC3B,4BAA4B;IAC5B,QAAQ,CAAC,KAAK,EAAE,UAAU,GAAG,cAAc,CAAC;IAC5C,qFAAqF;IACrF,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AAED,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB,sDAAsD,CAAC;AAEtF,2DAA2D;AAC3D,eAAO,MAAM,cAAc,EAAE,SAAS,WAAW,EAkBhD,CAAC;AAEF;;;;;;;;;;;GAWG;AACH,wBAAgB,YAAY,CAC1B,KAAK,EAAE,UAAU,GAAG,cAAc,EAClC,OAAO,EAAE,SAAS,aAAa,EAAE,GAChC,MAAM,CAUR"}

package/dist/memory/auto-row-rules.js

@@ -0,0 +1,55 @@
+/**
+ * The named auto-row rules (T13951) and the guard the memory accessors resolve
+ * from rule ids, so no caller hands the store raw SQL (T14003).
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ */
+import { stubObservationClause } from './brain-stub-prune.js';
+import { DISPATCH_TRACE_TEXT_PREFIX } from './dispatch-trace-format.js';
+/** Guard every rule shares: only current, unverified rows. */
+export const CURRENT_UNVERIFIED = 'invalid_at IS NULL AND COALESCE(verified, 0) != 1';
+/** The rules, each matching rows only machinery writes. */
+export const AUTO_ROW_RULES = [
+    {
+        id: 'dispatch-trace',
+        table: 'patterns',
+        predicate: `pattern LIKE '${DISPATCH_TRACE_TEXT_PREFIX}%'`,
+    },
+    {
+        // Both the title and the writer's JSON payload: a human note titled
+        // "Doc attached: ..." without the payload is never matched.
+        id: 'doc-attachment',
+        table: 'observations',
+        predicate: `title GLOB 'Doc attached:*' AND COALESCE(narrative, '') LIKE '%"kind":"doc-attachment"%'`,
+    },
+    {
+        id: 'task-stub',
+        table: 'observations',
+        predicate: `(${stubObservationClause()})`,
+    },
+];
+/**
+ * The SQL guard for a write: any of the named rules, on current unverified rows.
+ *
+ * @param table - Table being written.
+ * @param ruleIds - Rules the row must still match.
+ * @returns A predicate over unaliased columns.
+ * @throws Error when no rule is named, or a rule is unknown or reads another table.
+ * @example
+ * ```ts
+ * const guard = autoRowGuard('patterns', ['dispatch-trace']);
+ * ```
+ */
+export function autoRowGuard(table, ruleIds) {
+    const predicates = ruleIds.map((id) => {
+        const rule = AUTO_ROW_RULES.find((candidate) => candidate.id === id);
+        // @sync-invariant none:input-shape an unknown or mismatched rule is refused before any write
+        if (!rule || rule.table !== table)
+            throw new Error(`No auto-row rule '${id}' for ${table}`);
+        return `(${rule.predicate})`;
+    });
+    // @sync-invariant none:input-shape an empty guard is refused before any write
+    if (predicates.length === 0)
+        throw new Error(`An auto-row guard for ${table} names no rule`);
+    return `(${predicates.join(' OR ')}) AND ${CURRENT_UNVERIFIED}`;
+}
+//# sourceMappingURL=auto-row-rules.js.map

package/dist/memory/auto-row-rules.js.map

@@ -0,0 +1 @@
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package/dist/memory/brain-lifecycle.d.ts.map

@@ -1 +1 @@
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package/dist/memory/brain-lifecycle.js

@@ -21,6 +21,7 @@ import { getLogger } from '../logger.js';
 import { getBrainAccessor } from '../store/memory-accessor.js';
 import { typedAll } from '../store/typed-query.js';
 import { EDGE_TYPES } from './edge-types.js';
+import { autoRowExclusionClause } from './eligibility.js';
 /**
  * Apply temporal decay to brain_learnings confidence values.
  *
@@ -351,12 +352,16 @@ export async function runTierPromotion(projectRoot) {
         .slice(0, 19);
     // Tables + their date column name (mixed conventions in schema)
     const tables = [
-        { table: 'brain_observations', dateCol: 'created_at' },
-        { table: 'brain_learnings', dateCol: 'created_at' },
-        { table: 'brain_patterns', dateCol: 'extracted_at' },
-        { table: 'brain_decisions', dateCol: 'created_at' },
+        { table: 'brain_observations', kind: 'observations', dateCol: 'created_at' },
+        { table: 'brain_learnings', kind: 'learnings', dateCol: 'created_at' },
+        { table: 'brain_patterns', kind: 'patterns', dateCol: 'extracted_at' },
+        { table: 'brain_decisions', kind: 'decisions', dateCol: 'created_at' },
     ];
-    for (const { table, dateCol } of tables) {
+    for (const { table, kind, dateCol } of tables) {
+        // T13947: auto rows (dispatch traces, doc-attachment records, task stubs)
+        // are never promoted, whatever citation count they collected while reads
+        // still bumped it.
+        const notAuto = autoRowExclusionClause(kind);
         let shortToMedium = [];
         try {
             shortToMedium = typedAll(nativeDb.prepare(`
@@ -364,7 +369,7 @@ export async function runTierPromotion(projectRoot) {
           FROM ${table}
           WHERE memory_tier = 'short'
             AND invalid_at IS NULL
-            AND ${dateCol} < ?
+            AND ${dateCol} < ?${notAuto}
             AND (
               citation_count >= 3
               OR quality_score >= 0.7
@@ -409,7 +414,7 @@ export async function runTierPromotion(projectRoot) {
           FROM ${table}
           WHERE memory_tier = 'medium'
             AND invalid_at IS NULL
-            AND ${dateCol} < ?
+            AND ${dateCol} < ?${notAuto}
             AND (citation_count >= 5 OR verified = 1)
         `), age7d);
         }
@@ -525,7 +530,7 @@ export async function promoteObservationsToTyped(projectRoot, limit = 100, thres
           AND NOT EXISTS (
             SELECT 1 FROM brain_promotion_log p
             WHERE p.observation_id = o.id
-          )
+          )${autoRowExclusionClause('observations', 'o')}
         ORDER BY o.created_at DESC
         LIMIT ?
       `), limit);