fix(embed): thread write column into sumStaleChunkChars — sync cost gate followed the legacy predicate (#1262)

Review follow-up: the PR threaded the write-side column through
countStaleChunks/listStaleChunks but not sumStaleChunkChars, so the
sync cost gate counted an alt-column brain's fully-embedded corpus as
phantom backlog on every gate (inflating the --full estimate and the
deferred-mode backlog note). Both engines already share
buildStaleChunkWhere, so this is a type widening + one call-site
thread + a contrast assertion.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/cli.ts

@@ -54,7 +54,7 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'facts', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
@@ -991,8 +991,6 @@ const THIN_CLIENT_REFUSED_COMMANDS = new Set([
   // hint pointing at the routable MCP tools; per-subcommand splits are
   // a v0.31.x follow-up TODO.
   'takes', 'sources',
-  // #1867: fence-backfill edits local .md fences + stamps the local DB.
-  'facts',
   // v0.32 thin-client routing audit (Codex round 2 findings #2, #4):
   // - `pages` purge-deleted is admin+localOnly (operations.ts:856-864)
   // - `files` list / file_url MCP ops are localOnly (operations.ts:1769-1879)
@@ -1028,7 +1026,6 @@ const THIN_CLIENT_REFUSE_HINTS: Record<string, string> = {
   migrate: "migrate runs on the host's local engine. Run on the host machine.",
   'apply-migrations': 'schema migrations run on the host. SSH and run there.',
   'repair-jsonb': 'repair-jsonb operates on the local DB only.',
-  facts: 'facts fence-backfill edits local entity-page fences. Run on the host machine.',
   integrity: 'integrity scans local files. Run on the host machine.',
   serve: 'serve starts a server. Run on the host, not the thin client.',
   dream: 'dream runs the autopilot cycle on the host. `gbrain remote ping` queues one. (Native `gbrain dream` thin-client routing planned for v0.31.2.)',
@@ -1858,13 +1855,6 @@ async function handleCliOnly(command: string, args: string[]) {
         await runEdgesBackfill(engine, args);
         break;
       }
-      case 'facts': {
-        // #1867 — re-runnable fence-backfill for row_num-NULL legacy fact
-        // rows (idempotent v0_32_2 phase B, exposed as an operator command).
-        const { runFactsCommand } = await import('./commands/facts.ts');
-        await runFactsCommand(engine, args);
-        break;
-      }
       case 'whoknows': {
         // v0.33 (Issue #?): expertise + relationship-proximity routing.
         // MCP op `find_experts` (read-scoped) backs the same code path; CLI
@@ -2345,7 +2335,6 @@ TOOLS
   check-backlinks <check|fix> [dir]  Find/fix missing back-links across brain
   lint <dir|file> [--fix]            Catch LLM artifacts, placeholder dates, bad frontmatter
   orphans [--json] [--count]         Find pages with no inbound wikilinks
-  facts fence-backfill [--dry-run]   Fence legacy fact rows (row_num NULL) onto entity pages
   salience [--days N] [--kind P]     v0.29: pages ranked by emotional + activity salience
   anomalies [--since D] [--sigma N]  v0.29: cohort-based statistical anomalies (tag, type)
   transcripts recent [--days N]      v0.29: recent raw .txt transcripts (local-only)

src/commands/embed.ts

@@ -1,6 +1,7 @@
 import type { BrainEngine } from '../core/engine.ts';
 import { embedBatch, currentEmbeddingSignature } from '../core/embedding.ts';
-import type { ChunkInput } from '../core/types.ts';
+import type { ChunkInput, ResolvedColumn } from '../core/types.ts';
+import { resolveWriteColumnForEngine } from '../core/search/embedding-column.ts';
 import { chunkText } from '../core/chunkers/recursive.ts';
 import { createProgress, type ProgressReporter } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
@@ -183,8 +184,13 @@ export class EmbeddingDimMismatchError extends Error {
  * fresh-install bug class at the very first invocation instead of letting
  * the worker pool hammer N pages with raw 22000 errors.
  */
-async function preflightDimMismatch(engine: BrainEngine, dryRun: boolean): Promise<void> {
+async function preflightDimMismatch(engine: BrainEngine, dryRun: boolean, embeddingColumn?: ResolvedColumn): Promise<void> {
   if (dryRun) return; // dry-run never embeds, no risk
+  // #1262: an alt-column brain writes to `embeddingColumn`, not the legacy
+  // `embedding` column — the legacy column's dims are irrelevant, and the
+  // registry entry (validated at resolve time) pins the target's dims. Only
+  // the legacy default path needs the schema-vs-gateway dim comparison.
+  if (embeddingColumn && embeddingColumn.name !== 'embedding') return;
   const { readContentChunksEmbeddingDim, embeddingMismatchMessage } = await import('../core/embedding-dim-check.ts');
   const { getEmbeddingDimensions, getEmbeddingModel } = await import('../core/ai/gateway.ts');
   let existing;
@@ -238,7 +244,12 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
   // v0.37.11.0 (Lane D.2): pre-flight dim-mismatch check. Catches the headline
   // fresh-install bug class before the worker pool spends 20 parallel calls
   // hitting raw Postgres dimension errors.
-  await preflightDimMismatch(engine, !!opts.dryRun);
+  // #1262: resolve the write-side embedding column ONCE at the boundary
+  // (merged config + gateway model) and thread the descriptor through every
+  // upsertChunks / stale-scan below. undefined => legacy `embedding` column.
+  const embeddingColumn = await resolveWriteColumnForEngine(engine);
+
+  await preflightDimMismatch(engine, !!opts.dryRun, embeddingColumn);
 
   const result: EmbedResult = {
     embedded: 0,
@@ -253,7 +264,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     for (const s of opts.slugs) {
       if (isAborted(opts.signal)) break; // #1737: stop the per-slug loop on abort
       try {
-        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal);
+        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal, embeddingColumn);
       } catch (e: unknown) {
         serr(`  Error embedding ${s}: ${e instanceof Error ? e.message : e}`);
       }
@@ -347,7 +358,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
         catchUp: opts.catchUp,
         pacer,
         paceMaxConcurrency,
-      }, opts.signal);
+      }, opts.signal, embeddingColumn);
     } finally {
       // E1: surface pacing telemetry (human + structured) when pacing was on.
       const snap = pacer.snapshot();
@@ -376,7 +387,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     return result;
   }
   if (opts.slug) {
-    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal);
+    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal, embeddingColumn);
     return result;
   }
   throw new Error('No embed target specified. Pass { slug }, { slugs }, { all }, or { stale }.');
@@ -521,8 +532,13 @@ async function embedPage(
   result: EmbedResult,
   sourceId?: string,
   signal?: AbortSignal,
+  embeddingColumn?: ResolvedColumn,
 ) {
   const opts = sourceId ? { sourceId } : undefined;
+  // #1262: write-side descriptor rides only on WRITE calls (upsertChunks).
+  const chunkOpts = (sourceId || embeddingColumn)
+    ? { ...(sourceId && { sourceId }), ...(embeddingColumn && { embeddingColumn }) }
+    : undefined;
   const page = await engine.getPage(slug, opts);
   if (!page) {
     throw new Error(`Page not found: ${slug}`);
@@ -554,7 +570,7 @@ async function embedPage(
     }
 
     if (inputs.length > 0) {
-      await engine.upsertChunks(slug, inputs, opts);
+      await engine.upsertChunks(slug, inputs, chunkOpts);
       chunks = await engine.getChunks(slug, opts);
     }
   }
@@ -589,7 +605,7 @@ async function embedPage(
     token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
   }));
 
-  await engine.upsertChunks(slug, updated, opts);
+  await engine.upsertChunks(slug, updated, chunkOpts);
   // v0.41.31: stamp provenance so a later model/dims swap is detectable as
   // stale. embedPage is the per-slug path used by `gbrain embed <slug>` AND
   // by `gbrain sync`'s post-import embed step (runEmbedCore({slugs})).
@@ -622,6 +638,7 @@ async function embedAll(
     paceMaxConcurrency?: number;
   },
   signal?: AbortSignal,
+  embeddingColumn?: ResolvedColumn,
 ) {
   // v0.41.31: current embedding provenance signature. Stamped onto pages
   // when their chunks are (re)embedded so a later model/dimension swap is
@@ -644,7 +661,7 @@ async function embedAll(
     // D7: thread sourceId so `gbrain embed --stale --source X` actually scopes.
     // v0.41.18.0 (A13): thread batchSize/priority/catchUp into the stale path.
     // #1737: thread the external abort signal so the cycle embed phase bails.
-    return await embedAllStale(engine, sourceId, dryRun, result, onProgress, staleOpts, signature, signal);
+    return await embedAllStale(engine, sourceId, dryRun, result, onProgress, staleOpts, signature, signal, embeddingColumn);
   }
 
   // --all path: pacer (no-op when off). E-1: lower the worker count to the
@@ -725,7 +742,10 @@ async function embedAll(
         embedding: embeddingMap.get(c.chunk_index) ?? undefined,
         token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
       }));
-      await observed(pacer, () => engine.upsertChunks(page.slug, updated, pageOpts));
+      await observed(pacer, () => engine.upsertChunks(page.slug, updated, {
+        ...(pageSourceId && { sourceId: pageSourceId }),
+        ...(embeddingColumn && { embeddingColumn }),
+      }));
       // v0.41.31: stamp embedding provenance so a later model swap is
       // detectable as stale.
       await observed(pacer, () =>
@@ -805,10 +825,16 @@ async function embedAllStale(
   },
   signature?: string,
   externalSignal?: AbortSignal,
+  embeddingColumn?: ResolvedColumn,
 ) {
   // D7: thread sourceId so source-scoped runs only count + visit
   // that source's NULL embeddings.
-  const sourceOpt = sourceId ? { sourceId } : undefined;
+  // #1262: the stale predicate follows the write-side column — without it an
+  // alt-column brain would perpetually re-select (and re-pay for) chunks whose
+  // target column is already populated.
+  const sourceOpt = (sourceId || embeddingColumn)
+    ? { ...(sourceId && { sourceId }), ...(embeddingColumn && { embeddingColumn }) }
+    : undefined;
 
   // v0.41.31: re-embed pages whose embedding_signature drifted (model/dims
   // swap). dry-run must NOT mutate, so it counts signature-stale via the
@@ -967,6 +993,7 @@ async function embedAllStale(
             afterUpdatedAt,
           }),
           ...(sourceId && { sourceId }),
+          ...(embeddingColumn && { embeddingColumn }),
         }),
       );
       if (batch.length === 0) {
@@ -1019,7 +1046,10 @@ async function embedAllStale(
             embedding: staleIdxToEmbedding.get(c.chunk_index) ?? undefined,
             token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
           }));
-          await observed(pacer, () => engine.upsertChunks(slug, merged, { sourceId: keySourceId }));
+          await observed(pacer, () => engine.upsertChunks(slug, merged, {
+            sourceId: keySourceId,
+            ...(embeddingColumn && { embeddingColumn }),
+          }));
           // v0.41.31: stamp provenance after the page's chunks are embedded —
           // but only when EVERY chunk was stale (fully re-embedded this pass).
           // A partially-stale page keeps preserved chunks of unknown/old
@@ -1090,7 +1120,7 @@ async function embedAllStale(
   // as a clean run — re-running won't help until the underlying failure is fixed.
   if (staleOpts?.catchUp && !effectiveSignal.aborted && embedFailures > 0) {
     const remaining = await engine.countStaleChunks(
-      signature ? { signature, ...(sourceId ? { sourceId } : {}) } : (sourceId ? { sourceId } : undefined),
+      signature ? { signature, ...sourceOpt } : sourceOpt,
     );
     if (remaining > 0) {
       serr(`\n  [embed] catch-up finished but ${remaining} chunk(s) remain stale after ${embedFailures} embed failure(s). These are not embeddable as-is; re-running won't clear them until the underlying error is resolved.`);

src/commands/facts.ts

@@ -1,48 +0,0 @@
-/**
- * gbrain facts — fact-store maintenance surface (#1867).
- *
- * `fence-backfill` re-runs the v0_32_2 fence-backfill phase on demand.
- * Remote `extract_facts` deposits that predate the fence-write backstop
- * (and any legacy DB-only insert) leave `row_num IS NULL` rows that the
- * cycle extract_facts guard refuses to reconcile past — previously the
- * only remedy was the one-shot v0_32_2 migration, which the ledger marks
- * complete and never re-runs. The phase is idempotent (only touches
- * `row_num IS NULL` rows), so exposing it as a command is safe to re-run
- * any time the backlog reappears.
- */
-import type { BrainEngine } from '../core/engine.ts';
-import { setCliExitVerdict } from '../core/cli-force-exit.ts';
-import { phaseBFenceFacts } from './migrations/v0_32_2.ts';
-
-function printHelp(): void {
-  process.stderr.write(
-    `Usage: gbrain facts fence-backfill [--dry-run]\n\n` +
-      `Fence-backfill: appends every legacy fact row (row_num IS NULL) to its\n` +
-      `entity page's \`## Facts\` fence and stamps row_num + source_markdown_slug\n` +
-      `back onto the DB row. Idempotent — re-runs only pick up rows still\n` +
-      `missing a fence assignment. Clears the backlog that makes the cycle's\n` +
-      `extract_facts phase skip fence→DB reconciliation.\n\n` +
-      `  --dry-run   report what would be fenced; no FS or DB writes\n`,
-  );
-}
-
-export async function runFactsCommand(engine: BrainEngine, args: string[]): Promise<void> {
-  const sub = args[0];
-  if (!sub || sub === '--help' || sub === '-h') {
-    printHelp();
-    return;
-  }
-  if (sub !== 'fence-backfill') {
-    process.stderr.write(`Unknown facts subcommand: ${sub}\n`);
-    printHelp();
-    setCliExitVerdict(1);
-    return;
-  }
-
-  const dryRun = args.includes('--dry-run');
-  const result = await phaseBFenceFacts(engine, { dryRun });
-  process.stderr.write(
-    `fence-backfill: ${result.status}${result.detail ? ` — ${result.detail}` : ''}\n`,
-  );
-  if (result.status === 'failed') setCliExitVerdict(1);
-}

src/commands/migrations/v0_32_2.ts

@@ -39,7 +39,6 @@ import type { BrainEngine } from '../../core/engine.ts';
 import { loadConfig, toEngineConfig } from '../../core/config.ts';
 import { createEngine } from '../../core/engine-factory.ts';
 import { upsertFactRow, parseFactsFence } from '../../core/facts-fence.ts';
-import { resolvePageFilePath } from '../../core/markdown.ts';
 
 let testEngineOverride: BrainEngine | null = null;
 export function __setTestEngineOverride(engine: BrainEngine | null): void {
@@ -149,16 +148,9 @@ function isLocalPathDirty(localPath: string): boolean {
   }
 }
 
-/**
- * Exported (not just via `__testing`) because `gbrain facts fence-backfill`
- * (#1867) re-runs this phase on demand: remote `extract_facts` deposits that
- * predate the fence-write backstop leave row_num-NULL rows the cycle guard
- * refuses to reconcile past. The phase is idempotent (only touches
- * `row_num IS NULL` rows), so re-running is always safe.
- */
-export async function phaseBFenceFacts(
+async function phaseBFenceFacts(
   engine: BrainEngine | null,
-  opts: Pick<OrchestratorOpts, 'dryRun'>,
+  opts: OrchestratorOpts,
 ): Promise<OrchestratorPhaseResult> {
   if (opts.dryRun) {
     // Dry-run: report what WOULD happen without touching FS or DB.
@@ -246,11 +238,7 @@ export async function phaseBFenceFacts(
     for (const [key, group] of groups) {
       const [sourceId, entitySlug] = key.split('\0');
       const localPath = localPathById.get(sourceId)!;
-      // resolvePageFilePath, NOT a bare join — non-default sources fence
-      // into `<local_path>/.sources/<id>/<slug>.md`, the same path the
-      // fence-write backstop and put_page write-through compute. A bare
-      // join here diverges fence and DB for non-default sources (#2044).
-      const filePath = resolvePageFilePath(localPath, entitySlug, sourceId);
+      const filePath = join(localPath, `${entitySlug}.md`);
       const tmpPath = `${filePath}.tmp`;
 
       try {
@@ -281,21 +269,6 @@ export async function phaseBFenceFacts(
         const existingFence = parseFactsFence(body);
         const existingKeySet = new Set(existingFence.facts.map(f => `${f.claim}\0${f.source ?? ''}`));
 
-        // Seed appended row_nums from MAX(fence max, DB max) — same #2044
-        // divergence guard as writeFactsToFence. When the fence at the
-        // resolved path is missing/behind but the DB already holds stamped
-        // rows for this slug (legacy wrong-path fence writes), fence-max+1
-        // collides with idx_facts_fence_key on the post-rename UPDATE,
-        // failing the page and leaving fence and DB disagreeing.
-        const dbMaxRows = await engine.executeRaw<{ max: number | string | null }>(
-          `SELECT MAX(row_num) AS max FROM facts
-            WHERE source_id = $1 AND source_markdown_slug = $2`,
-          [sourceId, entitySlug],
-        );
-        const dbMaxRowNum = Number(dbMaxRows[0]?.max ?? 0) || 0;
-        const fenceMaxRowNum = existingFence.facts.reduce((m, f) => Math.max(m, f.rowNum), 0);
-        let nextRowNum = Math.max(fenceMaxRowNum, dbMaxRowNum) + 1;
-
         const assignments: Array<{ id: string; row_num: number }> = [];
         for (const row of group) {
           const key = `${row.fact}\0${row.source ?? ''}`;
@@ -318,7 +291,6 @@ export async function phaseBFenceFacts(
                 .toISOString().slice(0, 10)
             : undefined;
           const { body: updated, rowNum } = upsertFactRow(body, {
-            rowNum:     nextRowNum++,
             claim:      row.fact,
             kind:       row.kind,
             confidence: row.confidence,
@@ -409,7 +381,7 @@ async function phaseCVerify(
     for (const g of groups) {
       const localPath = localPathById.get(g.source_id);
       if (!localPath) continue;
-      const filePath = resolvePageFilePath(localPath, g.source_markdown_slug, g.source_id);
+      const filePath = join(localPath, `${g.source_markdown_slug}.md`);
       if (!existsSync(filePath)) {
         mismatches.push(`${g.source_markdown_slug} (file missing)`);
         continue;

src/commands/sync.ts

@@ -576,9 +576,16 @@ async function runInlineCostGate(
 
   // Stale backlog: cheap single SQL; fail-open to 0 so a transient DB hiccup
   // never blocks the sync. Signature-aware (model/dims swap surfaces here).
+  // #1262: follow the write-side embedding column — otherwise an alt-column
+  // brain's fully-embedded corpus counts as phantom backlog on every gate.
   let staleChars = 0;
   try {
-    staleChars = await engine.sumStaleChunkChars({ signature: currentEmbeddingSignature() });
+    const { resolveWriteColumnForEngine } = await import('../core/search/embedding-column.ts');
+    const embeddingColumn = await resolveWriteColumnForEngine(engine);
+    staleChars = await engine.sumStaleChunkChars({
+      signature: currentEmbeddingSignature(),
+      ...(embeddingColumn && { embeddingColumn }),
+    });
   } catch {
     staleChars = 0;
   }

src/core/contextual-retrieval-service.ts

@@ -61,6 +61,7 @@ import {
   type SynopsisFailureKind,
 } from './audit-synopsis.ts';
 import type { BrainEngine } from './engine.ts';
+import { resolveWriteColumnForEngine } from './search/embedding-column.ts';
 import type { ChunkInput, CRMode, Page } from './types.ts';
 import type { SourceRow } from './sources-ops.ts';
 
@@ -286,9 +287,13 @@ export async function reembedPageWithContextualRetrieval(
 
       // ── PHASE 2: single DB transaction ───────────────────────────
       try {
+        // #1262: contextual re-embeds write TEXT embeddings — thread the
+        // caller-resolved write column like every other embed path.
+        const embeddingColumn = await resolveWriteColumnForEngine(args.engine);
         await args.engine.transaction(async (tx) => {
           await tx.upsertChunks(args.pageSlug, phase1.embeddedChunks, {
             sourceId: args.sourceId,
+            ...(embeddingColumn && { embeddingColumn }),
           });
           await tx.updatePageContextualRetrievalState(
             args.pageSlug,

src/core/cycle/extract-facts.ts

@@ -176,11 +176,9 @@ export async function runExtractFacts(
   if (legacyCount > 0) {
     result.guardTriggered = true;
     result.warnings.push(
-      `extract_facts: ${legacyCount} legacy fact rows pending fence backfill ` +
-      `(row_num IS NULL — v0.31 rows or remote extract_facts deposits that ` +
-      `predate the fence backstop). Run \`gbrain facts fence-backfill\` ` +
-      `(idempotent, re-runnable) before this phase can safely reconcile ` +
-      `fence → DB.`,
+      `extract_facts: ${legacyCount} legacy v0.31 fact rows pending fence backfill. ` +
+      `Run \`gbrain apply-migrations --yes\` to complete v0_32_2 before this phase ` +
+      `can safely reconcile fence → DB.`,
     );
     return result;
   }

src/core/embed-stale.ts

@@ -18,7 +18,7 @@
  */
 
 import type { BrainEngine } from './engine.ts';
-import type { ChunkInput } from './types.ts';
+import type { ChunkInput, ResolvedColumn } from './types.ts';
 import { embedBatchWithBackoff } from '../commands/embed.ts';
 import { type DbPacer, createNoopPacer, observed } from './db-pacer.ts';
 import { AbortError } from './abort-check.ts';
@@ -61,6 +61,13 @@ export interface EmbedStaleOpts {
    * Omit to keep the legacy `embedding IS NULL`-only behavior.
    */
   embeddingSignature?: string;
+  /**
+   * #1262: caller-resolved write-side embedding column. Threaded into BOTH
+   * listStaleChunks (staleness predicate) and upsertChunks (write target) so
+   * an alt-column brain converges instead of re-selecting embedded rows.
+   * Resolve at the boundary via `resolveWriteColumnForEngine()`.
+   */
+  embeddingColumn?: ResolvedColumn;
   /**
    * DB-contention pacer (paced-backfill). When enabled it (a) supplies the
    * worker count via the caller passing `concurrency = bundle.maxConcurrency`
@@ -156,6 +163,7 @@ export async function embedStaleForSource(
         afterPageId,
         afterChunkIndex,
         sourceId,
+        ...(opts.embeddingColumn && { embeddingColumn: opts.embeddingColumn }),
       }),
     );
     if (batch.length === 0) {
@@ -223,7 +231,10 @@ export async function embedStaleForSource(
           doc_comment: c.doc_comment ?? undefined,
           symbol_name_qualified: c.symbol_name_qualified ?? undefined,
         }));
-        await observed(pacer, () => engine.upsertChunks(slug, merged, { sourceId: keySourceId }));
+        await observed(pacer, () => engine.upsertChunks(slug, merged, {
+          sourceId: keySourceId,
+          ...(opts.embeddingColumn && { embeddingColumn: opts.embeddingColumn }),
+        }));
         // v0.41.31: stamp provenance only when EVERY chunk was stale (fully
         // re-embedded this pass) — a partially-stale page keeps preserved
         // chunks of unknown provenance, so don't claim current. After the

src/core/engine.ts

@@ -12,6 +12,7 @@ import type {
   BrainStats, BrainHealth,
   IngestLogEntry, IngestLogInput,
   EngineConfig,
+  ResolvedColumn,
   CodeEdgeInput, CodeEdgeResult,
   EvalCandidate, EvalCandidateInput,
   EvalCaptureFailure, EvalCaptureFailureReason,
@@ -987,8 +988,13 @@ export interface BrainEngine {
    * — Postgres rolls back automatically on conn drop, so commit-ambiguous
    * failure replays to the same end state. Callers MUST NOT wrap externally;
    * see {@link BatchOpts} retry-contract block.
+   *
+   * `opts.embeddingColumn` (optional) selects the content_chunks column that
+   * receives TEXT embeddings (#1262). The caller resolves the descriptor at
+   * the import/embed boundary via `resolveWriteColumn()`; engines never read
+   * config or choose columns themselves. Omitted => legacy `embedding`.
    */
-  upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string } & BatchOpts): Promise<void>;
+  upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string; embeddingColumn?: ResolvedColumn } & BatchOpts): Promise<void>;
   /**
    * Read every chunk for a page. `opts.sourceId` source-scopes the page
    * lookup; without it, multi-source brains return chunks from every
@@ -1005,8 +1011,13 @@ export interface BrainEngine {
    * counts across every source in the brain. Operators running
    * `gbrain embed --stale --source media-corpus` expect only that
    * source's NULLs touched; the caller threads `sourceId` here.
+   *
+   * `opts.embeddingColumn` switches the staleness predicate from the legacy
+   * `embedding` column to the resolved write-side column, so alt-column
+   * brains do not perpetually re-select rows whose target column is already
+   * populated (#1262). Must match the eventual upsertChunks target.
    */
-  countStaleChunks(opts?: { sourceId?: string; signature?: string }): Promise<number>;
+  countStaleChunks(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number>;
   /**
    * Sum of LENGTH(chunk_text) over stale chunks — the character-count
    * backlog the embed phase / embed-backfill will process. Sibling of
@@ -1020,8 +1031,13 @@ export interface BrainEngine {
    * model signature (a model/dims swap). NULL signature is GRANDFATHERED
    * (never counted) so the post-migration corpus isn't flagged en masse.
    * Omit `signature` for the legacy `embedding IS NULL`-only count.
+   *
+   * `opts.embeddingColumn` switches the staleness predicate to the resolved
+   * write-side column (#1262) — same contract as countStaleChunks — so the
+   * sync cost gate doesn't count an alt-column brain's fully-embedded corpus
+   * as phantom backlog.
    */
-  sumStaleChunkChars(opts?: { sourceId?: string; signature?: string }): Promise<number>;
+  sumStaleChunkChars(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number>;
   /**
    * Stamp `pages.embedding_signature = signature` for one page. Called after
    * a page's chunks are (re)embedded so a later model swap can detect it as
@@ -1069,6 +1085,9 @@ export interface BrainEngine {
     // both round-trip TIMESTAMPTZ as Date | string; ISO string is the
     // common denominator on the wire).
     afterUpdatedAt?: string | null;
+    // #1262: staleness predicate targets this column when set (must match
+    // countStaleChunks and the eventual upsertChunks write target).
+    embeddingColumn?: ResolvedColumn;
   }): Promise<StaleChunkRow[]>;
   /**
    * Delete every chunk for a page. Internal page-id lookup is sourceId-scoped
@@ -1739,14 +1758,13 @@ export interface BrainEngine {
    * single-row supersede flow because fence reconciliation is the canonical
    * source-of-truth direction, not the consolidator path.
    *
-   * Insertion runs in a single transaction. A collision on the v51
-   * partial UNIQUE index `(source_id, source_markdown_slug, row_num)`
-   * skips ONLY that row (ON CONFLICT DO NOTHING, #2044) — the rest of
-   * the batch still commits, so a redundant deposit against an
-   * already-indexed fence row is idempotent instead of a hard failure.
+   * Insertion is atomic per call: all rows commit in a single transaction
+   * or none commit (the transaction rolls back on any constraint
+   * violation, e.g. the v51 partial UNIQUE index on
+   * `(source_id, source_markdown_slug, row_num)`).
    *
-   * Returns the inserted ids in input-order (colliding rows omitted) so
-   * callers can correlate fence-row → DB-id without a separate lookup.
+   * Returns the inserted ids in input-order so callers can correlate
+   * fence-row → DB-id without a separate lookup.
    */
   insertFacts(
     rows: Array<NewFact & { row_num: number; source_markdown_slug: string }>,

src/core/facts/fence-write.ts

@@ -218,27 +218,11 @@ export async function writeFactsToFence(
       }
 
       // 2. Upsert each fact onto the fence in input order. row_num
-      //    monotonically increases, append-only, seeded from the MAX of
-      //    the fence and the DB index (#2044): when fence and DB have
-      //    diverged (e.g. legacy writes that stamped DB rows against a
-      //    fence at a path this code no longer reads), fence-max+1 can
-      //    collide with an existing DB row_num, tripping
-      //    idx_facts_fence_key and rolling back the whole batch.
-      const dbMaxRows = await engine.executeRaw<{ max: number | string | null }>(
-        `SELECT MAX(row_num) AS max FROM facts
-          WHERE source_id = $1 AND source_markdown_slug = $2`,
-        [target.sourceId, target.slug],
-      );
-      const dbMaxRowNum = Number(dbMaxRows[0]?.max ?? 0) || 0;
-      const fenceMaxRowNum = parseFactsFence(body).facts
-        .reduce((m, f) => Math.max(m, f.rowNum), 0);
-      let nextRowNum = Math.max(fenceMaxRowNum, dbMaxRowNum) + 1;
-
+      //    monotonically increases (max-existing + 1 per call, append-only).
       const assignedRowNums: number[] = [];
       for (const f of facts) {
         const validFromStr = (f.validFrom ?? new Date()).toISOString().slice(0, 10);
         const { body: updated, rowNum } = upsertFactRow(body, {
-          rowNum:      nextRowNum++,
           claim:       f.fact,
           kind:        (f.kind ?? 'fact') as 'fact' | 'event' | 'preference' | 'commitment' | 'belief',
           confidence:  f.confidence ?? 1.0,

src/core/import-file.ts

@@ -10,7 +10,8 @@ import { findChunkForOffset } from './chunkers/edge-extractor.ts';
 import { extractCodeRefs, imageOfCandidates } from './link-extraction.ts';
 import { embedBatch, embedMultimodal, currentEmbeddingSignature } from './embedding.ts';
 import { slugifyPath, slugifyCodePath, isCodeFilePath } from './sync.ts';
-import type { ChunkInput, PageInput, PageType } from './types.ts';
+import type { ChunkInput, PageInput, PageType, ResolvedColumn } from './types.ts';
+import { resolveWriteColumnForEngine } from './search/embedding-column.ts';
 import { computeEffectiveDate } from './effective-date.ts';
 import { MARKDOWN_CHUNKER_VERSION } from './chunkers/recursive.ts';
 import { logSlugFallback } from './audit-slug-fallback.ts';
@@ -740,6 +741,14 @@ export async function importFromContent(
   // schema DEFAULT — required for multi-source brains; harmless ('default')
   // for single-source callers.
   const txOpts = sourceId ? { sourceId } : undefined;
+  // #1262: resolve the write-side embedding column once (merged config +
+  // gateway model) BEFORE the transaction; the descriptor rides only on
+  // upsertChunks so text embeddings land in the registered column.
+  const chunkWriteColumn = await resolveWriteColumnForEngine(engine);
+  const chunkOpts: { sourceId?: string; embeddingColumn?: ResolvedColumn } | undefined =
+    (sourceId || chunkWriteColumn)
+      ? { ...(sourceId && { sourceId }), ...(chunkWriteColumn && { embeddingColumn: chunkWriteColumn }) }
+      : undefined;
   await engine.transaction(async (tx) => {
     if (existing) await tx.createVersion(slug, txOpts);
 
@@ -824,7 +833,7 @@ export async function importFromContent(
     }
 
     if (chunks.length > 0) {
-      await tx.upsertChunks(slug, chunks, txOpts);
+      await tx.upsertChunks(slug, chunks, chunkOpts);
       // v0.41.31: stamp embedding provenance when this import actually
       // embedded (not --no-embed), so a later model/dims swap is detectable
       // as stale via embed --stale. The deferred/backfill + per-slug embed
@@ -1064,6 +1073,12 @@ export async function importCodeFile(
   const title = `${relativePath} (${lang})`;
   const sourceId = opts.sourceId;
   const txOpts = sourceId ? { sourceId } : undefined;
+  // #1262: write-side embedding column descriptor (rides only on upsertChunks).
+  const chunkWriteColumn = await resolveWriteColumnForEngine(engine);
+  const chunkOpts: { sourceId?: string; embeddingColumn?: ResolvedColumn } | undefined =
+    (sourceId || chunkWriteColumn)
+      ? { ...(sourceId && { sourceId }), ...(chunkWriteColumn && { embeddingColumn: chunkWriteColumn }) }
+      : undefined;
 
   const byteLength = Buffer.byteLength(content, 'utf-8');
   if (byteLength > MAX_FILE_SIZE) {
@@ -1183,7 +1198,7 @@ export async function importCodeFile(
     await tx.addTag(slug, lang, txOpts);
 
     if (chunks.length > 0) {
-      await tx.upsertChunks(slug, chunks, txOpts);
+      await tx.upsertChunks(slug, chunks, chunkOpts);
       // v0.41.31: stamp embedding provenance ONLY when every chunk was
       // freshly embedded with the current model this call (no reuse-by-hash
       // carrying old-model vectors). Mixed pages stay unstamped rather than
@@ -1332,6 +1347,12 @@ export async function withImportTransaction(
 ): Promise<void> {
   const sourceId = spec.sourceId ?? 'default';
   const txOpts = spec.sourceId ? { sourceId: spec.sourceId } : undefined;
+  // #1262: write-side embedding column descriptor (rides only on upsertChunks).
+  const chunkWriteColumn = await resolveWriteColumnForEngine(engine);
+  const chunkOpts: { sourceId?: string; embeddingColumn?: ResolvedColumn } | undefined =
+    (spec.sourceId || chunkWriteColumn)
+      ? { ...(spec.sourceId && { sourceId: spec.sourceId }), ...(chunkWriteColumn && { embeddingColumn: chunkWriteColumn }) }
+      : undefined;
   await engine.transaction(async (tx) => {
     if (spec.hadExisting) await tx.createVersion(spec.slug, txOpts);
     await tx.putPage(spec.slug, spec.page, txOpts);
@@ -1347,7 +1368,7 @@ export async function withImportTransaction(
     }
     if (spec.chunks !== undefined) {
       if (spec.chunks.length > 0) {
-        await tx.upsertChunks(spec.slug, spec.chunks, txOpts);
+        await tx.upsertChunks(spec.slug, spec.chunks, chunkOpts);
       } else {
         await tx.deleteChunks(spec.slug, txOpts);
       }

src/core/minions/handlers/embed-backfill.ts

@@ -35,6 +35,7 @@ import { tryAcquireDbLock } from '../../db-lock.ts';
 import { BudgetTracker, BudgetExhausted } from '../../budget/budget-tracker.ts';
 import { withBudgetTracker } from '../../ai/gateway.ts';
 import { embedStaleForSource } from '../../embed-stale.ts';
+import { resolveWriteColumnForEngine } from '../../search/embedding-column.ts';
 import { currentEmbeddingSignature } from '../../embedding.ts';
 import { type DbPacer, createDbPacer, createNoopPacer } from '../../db-pacer.ts';
 import { resolvePaceMode, loadPaceModeConfig, readPaceEnv } from '../../pace-mode.ts';
@@ -164,12 +165,16 @@ export function makeEmbedBackfillHandler(engine: BrainEngine) {
     // the supervisor, so pacing it is the headline win.
     const { pacer, concurrency } = await resolveBackfillPacer(engine, job.data);
 
+    // #1262: resolve the write-side embedding column once at the job boundary.
+    const embeddingColumn = await resolveWriteColumnForEngine(engine);
+
     try {
       const result = await withBudgetTracker(tracker, async () =>
         embedStaleForSource(engine, sourceId, {
           batchSize,
           signal: job.signal,
           pacer,
+          ...(embeddingColumn && { embeddingColumn }),
           ...(concurrency !== undefined && { concurrency }),
           // v0.41.31: re-embed pages whose model signature drifted + stamp
           // provenance as chunks land.

src/core/pglite-engine.ts

@@ -40,6 +40,7 @@ import type {
   BrainStats, BrainHealth,
   IngestLogEntry, IngestLogInput,
   EngineConfig,
+  ResolvedColumn,
   EvalCandidate, EvalCandidateInput,
   EvalCaptureFailure, EvalCaptureFailureReason,
   SalienceOpts, SalienceResult, AnomaliesOpts, AnomalyResult,
@@ -2230,12 +2231,20 @@ export class PGLiteEngine implements BrainEngine {
   }
 
   // Chunks
-  async upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string } & BatchOpts): Promise<void> {
+  async upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string; embeddingColumn?: ResolvedColumn } & BatchOpts): Promise<void> {
     return this.batchRetry(opts?.auditSite ?? 'upsertChunks', opts?.signal, () => this._upsertChunksOnce(slug, chunks, opts), chunks.length);
   }
 
-  private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string }): Promise<void> {
+  private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string; embeddingColumn?: ResolvedColumn }): Promise<void> {
     const sourceId = opts?.sourceId ?? 'default';
+    // #1262: caller-resolved write target for TEXT embeddings. Descriptor
+    // names are identifier-validated + quoted by buildVectorCastFragment;
+    // omitted => legacy `embedding vector`. Mirrors postgres-engine.ts.
+    const targetFragment = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn)
+      : undefined;
+    const targetCol = targetFragment?.col ?? 'embedding';
+    const embeddingCast = targetFragment?.castSql.replace('$1::', '') ?? 'vector';
 
     // Source-scope the page-id lookup so duplicate slugs in different sources
     // do not return multiple rows or target the wrong page.
@@ -2270,7 +2279,7 @@ export class PGLiteEngine implements BrainEngine {
     // list. Image chunks pass embedding=null + embedding_image=Float32Array
     // (1024-dim Voyage). Text/code chunks pass embedding=Float32Array +
     // embedding_image=null. Default modality='text' when omitted.
-    const cols = '(page_id, chunk_index, chunk_text, chunk_source, embedding, model, token_count, embedded_at, language, symbol_name, symbol_type, start_line, end_line, parent_symbol_path, doc_comment, symbol_name_qualified, modality, embedding_image)';
+    const cols = `(page_id, chunk_index, chunk_text, chunk_source, ${targetCol}, model, token_count, embedded_at, language, symbol_name, symbol_type, start_line, end_line, parent_symbol_path, doc_comment, symbol_name_qualified, modality, embedding_image)`;
     const rowParts: string[] = [];
     const params: unknown[] = [];
     let paramIdx = 1;
@@ -2288,7 +2297,7 @@ export class PGLiteEngine implements BrainEngine {
       const modality = chunk.modality ?? 'text';
 
       // Inline ::vector NULL literals to avoid a per-branch placeholder.
-      const embeddingPh = embeddingStr ? `$${paramIdx++}::vector` : 'NULL';
+      const embeddingPh = embeddingStr ? `$${paramIdx++}::${embeddingCast}` : 'NULL';
       const embeddedAtPh = embeddingStr ? 'now()' : 'NULL';
       const embeddingImagePh = embeddingImageStr ? `$${paramIdx++}::vector` : 'NULL';
 
@@ -2327,19 +2336,19 @@ export class PGLiteEngine implements BrainEngine {
        ON CONFLICT (page_id, chunk_index) DO UPDATE SET
          chunk_text = EXCLUDED.chunk_text,
          chunk_source = EXCLUDED.chunk_source,
-         embedding = CASE
-           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text THEN EXCLUDED.embedding
-           WHEN content_chunks.embedding IS NULL THEN EXCLUDED.embedding
+         ${targetCol} = CASE
+           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text THEN EXCLUDED.${targetCol}
+           WHEN content_chunks.${targetCol} IS NULL THEN EXCLUDED.${targetCol}
            WHEN EXCLUDED.embedded_at IS NOT NULL
                 AND (content_chunks.embedded_at IS NULL OR EXCLUDED.embedded_at > content_chunks.embedded_at)
-                THEN EXCLUDED.embedding
-           ELSE content_chunks.embedding
+                THEN EXCLUDED.${targetCol}
+           ELSE content_chunks.${targetCol}
          END,
          model = COALESCE(EXCLUDED.model, content_chunks.model),
          token_count = EXCLUDED.token_count,
          embedded_at = CASE
-           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text AND EXCLUDED.embedding IS NULL THEN NULL
-           WHEN content_chunks.embedding IS NULL AND EXCLUDED.embedding IS NOT NULL THEN EXCLUDED.embedded_at
+           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text AND EXCLUDED.${targetCol} IS NULL THEN NULL
+           WHEN content_chunks.${targetCol} IS NULL AND EXCLUDED.${targetCol} IS NOT NULL THEN EXCLUDED.embedded_at
            WHEN EXCLUDED.embedded_at IS NOT NULL
                 AND (content_chunks.embedded_at IS NULL OR EXCLUDED.embedded_at > content_chunks.embedded_at)
                 THEN EXCLUDED.embedded_at
@@ -2377,14 +2386,19 @@ export class PGLiteEngine implements BrainEngine {
    * drift (NULL grandfathered → never stale). Shared by countStaleChunks +
    * sumStaleChunkChars so they can't drift.
    */
-  private buildStaleChunkWhere(opts?: { sourceId?: string; signature?: string }): { where: string; params: unknown[] } {
+  private buildStaleChunkWhere(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): { where: string; params: unknown[] } {
+    // #1262: staleness targets the caller-resolved write column when set
+    // (identifier-validated + quoted); legacy `embedding` otherwise.
+    const staleCol = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn).col
+      : 'embedding';
     const params: unknown[] = [];
     const conds: string[] = [];
     if (opts?.signature !== undefined) {
       params.push(opts.signature);
-      conds.push(`(cc.embedding IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $${params.length}))`);
+      conds.push(`(cc.${staleCol} IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $${params.length}))`);
     } else {
-      conds.push(`cc.embedding IS NULL`);
+      conds.push(`cc.${staleCol} IS NULL`);
     }
     conds.push(`NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')`);
     if (opts?.sourceId !== undefined) {
@@ -2394,7 +2408,7 @@ export class PGLiteEngine implements BrainEngine {
     return { where: conds.join(' AND '), params };
   }
 
-  async countStaleChunks(opts?: { sourceId?: string; signature?: string }): Promise<number> {
+  async countStaleChunks(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number> {
     // D7: source-scoped count for `gbrain embed --stale --source X`. Always
     // JOIN pages so embed-skip + signature predicates apply. PGLite is
     // PostgreSQL 17.5 in WASM and supports the full JSONB operator set.
@@ -2410,7 +2424,7 @@ export class PGLiteEngine implements BrainEngine {
     return Number(count);
   }
 
-  async sumStaleChunkChars(opts?: { sourceId?: string; signature?: string }): Promise<number> {
+  async sumStaleChunkChars(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number> {
     // Sibling of countStaleChunks: same stale predicate, summing chunk_text
     // length for the sync cost preview. ::bigint guards int4 overflow.
     const { where, params } = this.buildStaleChunkWhere(opts);
@@ -2463,11 +2477,17 @@ export class PGLiteEngine implements BrainEngine {
     sourceId?: string;
     orderBy?: 'page_id' | 'updated_desc';
     afterUpdatedAt?: string | null;
+    embeddingColumn?: ResolvedColumn;
   }): Promise<StaleChunkRow[]> {
     const limit = opts?.batchSize ?? 2000;
     const afterPid = opts?.afterPageId ?? 0;
     const afterIdx = opts?.afterChunkIndex ?? -1;
     const orderBy = opts?.orderBy ?? 'page_id';
+    // #1262: staleness follows the caller-resolved write column (validated +
+    // quoted identifier); legacy `embedding` otherwise.
+    const staleCol = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn).col
+      : 'embedding';
 
     // v0.41.18.0 (A13, codex #9): --priority recent path. See postgres-engine
     // sibling for full rationale. Same composite cursor + ORDER BY.
@@ -2481,7 +2501,7 @@ export class PGLiteEngine implements BrainEngine {
                   p.updated_at
              FROM content_chunks cc
              JOIN pages p ON p.id = cc.page_id
-            WHERE cc.embedding IS NULL
+            WHERE cc.${staleCol} IS NULL
               AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             ORDER BY p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC
             LIMIT $1`,
@@ -2492,7 +2512,7 @@ export class PGLiteEngine implements BrainEngine {
                   p.updated_at
              FROM content_chunks cc
              JOIN pages p ON p.id = cc.page_id
-            WHERE cc.embedding IS NULL
+            WHERE cc.${staleCol} IS NULL
               AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
               AND (
                 p.updated_at < $1::timestamptz
@@ -2511,7 +2531,7 @@ export class PGLiteEngine implements BrainEngine {
                 p.updated_at
            FROM content_chunks cc
            JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE cc.${staleCol} IS NULL
             AND p.source_id = $1
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
           ORDER BY p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC
@@ -2523,7 +2543,7 @@ export class PGLiteEngine implements BrainEngine {
                 p.updated_at
            FROM content_chunks cc
            JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE cc.${staleCol} IS NULL
             AND p.source_id = $1
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             AND (
@@ -2548,7 +2568,7 @@ export class PGLiteEngine implements BrainEngine {
                 cc.model, cc.token_count, p.source_id, cc.page_id
            FROM content_chunks cc
            JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE cc.${staleCol} IS NULL
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             AND (cc.page_id, cc.chunk_index) > ($1, $2)
           ORDER BY cc.page_id, cc.chunk_index
@@ -2562,7 +2582,7 @@ export class PGLiteEngine implements BrainEngine {
               cc.model, cc.token_count, p.source_id, cc.page_id
          FROM content_chunks cc
          JOIN pages p ON p.id = cc.page_id
-        WHERE cc.embedding IS NULL
+        WHERE cc.${staleCol} IS NULL
           AND p.source_id = $1
           AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
           AND (cc.page_id, cc.chunk_index) > ($2, $3)
@@ -4102,13 +4122,11 @@ export class PGLiteEngine implements BrainEngine {
   ): Promise<{ inserted: number; ids: number[] }> {
     if (rows.length === 0) return { inserted: 0, ids: [] };
 
-    // Single transaction; per-row INSERTs (not multi-row VALUES) keep the
-    // embedding-vs-no-embedding branching readable; batch sizes are small
-    // (5-30 rows per page in practice) so the loop overhead is negligible
-    // vs the embedding compute cost. #2044: ON CONFLICT DO NOTHING on the
-    // v51 partial UNIQUE index makes a residual fence/DB row_num collision
-    // skip that row instead of rolling back the whole batch (parity with
-    // postgres-engine.ts).
+    // Single transaction so the v51 partial UNIQUE index can roll back the
+    // whole batch on constraint violation. Per-row INSERTs (not multi-row
+    // VALUES) keep the embedding-vs-no-embedding branching readable; batch
+    // sizes are small (5-30 rows per page in practice) so the loop overhead
+    // is negligible vs the embedding compute cost.
     const ids = await this.db.transaction(async (tx) => {
       const out: number[] = [];
       for (const input of rows) {
@@ -4151,11 +4169,7 @@ export class PGLiteEngine implements BrainEngine {
                  $14, $15,
                  $16, $17, $18, $19,
                  $20
-               )
-               ON CONFLICT (source_id, source_markdown_slug, row_num)
-                 WHERE row_num IS NOT NULL
-                 DO NOTHING
-               RETURNING id`
+               ) RETURNING id`
             : `INSERT INTO facts (
                  source_id, entity_slug, fact, kind, visibility, notability, context,
                  valid_from, valid_until, source, source_session, confidence,
@@ -4169,16 +4183,12 @@ export class PGLiteEngine implements BrainEngine {
                  $15, $16,
                  $17, $18, $19, $20,
                  $21
-               )
-               ON CONFLICT (source_id, source_markdown_slug, row_num)
-                 WHERE row_num IS NOT NULL
-                 DO NOTHING
-               RETURNING id`,
+               ) RETURNING id`,
           embedStr === null
             ? [ctx.source_id, entitySlug, input.fact, kind, visibility, notability, context, validFrom, validUntil, input.source, sourceSession, confidence, embeddedAt, input.row_num, input.source_markdown_slug, claimMetric, claimValue, claimUnit, claimPeriod, eventType]
             : [ctx.source_id, entitySlug, input.fact, kind, visibility, notability, context, validFrom, validUntil, input.source, sourceSession, confidence, embedStr, embeddedAt, input.row_num, input.source_markdown_slug, claimMetric, claimValue, claimUnit, claimPeriod, eventType],
         );
-        if (ins.rows[0]) out.push(ins.rows[0].id);
+        out.push(ins.rows[0].id);
       }
       return out;
     });

src/core/postgres-engine.ts

@@ -50,6 +50,7 @@ import type {
   BrainStats, BrainHealth,
   IngestLogEntry, IngestLogInput,
   EngineConfig,
+  ResolvedColumn,
   EvalCandidate, EvalCandidateInput,
   EvalCaptureFailure, EvalCaptureFailureReason,
   SalienceOpts, SalienceResult, AnomaliesOpts, AnomalyResult,
@@ -2380,13 +2381,21 @@ export class PostgresEngine implements BrainEngine {
   }
 
   // Chunks
-  async upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string } & BatchOpts): Promise<void> {
+  async upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string; embeddingColumn?: ResolvedColumn } & BatchOpts): Promise<void> {
     return this.batchRetry(opts?.auditSite ?? 'upsertChunks', opts?.signal, () => this._upsertChunksOnce(slug, chunks, opts), chunks.length);
   }
 
-  private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string }): Promise<void> {
+  private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string; embeddingColumn?: ResolvedColumn }): Promise<void> {
     const sql = this.sql;
     const sourceId = opts?.sourceId ?? 'default';
+    // #1262: caller-resolved write target for TEXT embeddings. Descriptor
+    // names are identifier-validated + quoted by buildVectorCastFragment;
+    // omitted => legacy `embedding vector`.
+    const targetFragment = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn)
+      : undefined;
+    const targetCol = targetFragment?.col ?? 'embedding';
+    const embeddingCast = targetFragment?.castSql.replace('$1::', '') ?? 'vector';
 
     // Source-scope the page-id lookup. Without this filter, multi-source
     // brains where the slug exists in 2+ sources return >1 row and the
@@ -2413,7 +2422,7 @@ export class PostgresEngine implements BrainEngine {
     // scope metadata through upserts.
     // v0.27.1 (Phase 8): added `modality` + `embedding_image` to the column
     // list. Image chunks pass embedding=null + embedding_image=Float32Array.
-    const cols = '(page_id, chunk_index, chunk_text, chunk_source, embedding, model, token_count, embedded_at, language, symbol_name, symbol_type, start_line, end_line, parent_symbol_path, doc_comment, symbol_name_qualified, modality, embedding_image)';
+    const cols = `(page_id, chunk_index, chunk_text, chunk_source, ${targetCol}, model, token_count, embedded_at, language, symbol_name, symbol_type, start_line, end_line, parent_symbol_path, doc_comment, symbol_name_qualified, modality, embedding_image)`;
     const rows: string[] = [];
     const params: unknown[] = [];
     let paramIdx = 1;
@@ -2430,7 +2439,7 @@ export class PostgresEngine implements BrainEngine {
         : null;
       const modality = chunk.modality ?? 'text';
 
-      const embeddingPh = embeddingStr ? `$${paramIdx++}::vector` : 'NULL';
+      const embeddingPh = embeddingStr ? `$${paramIdx++}::${embeddingCast}` : 'NULL';
       const embeddedAtPh = embeddingStr ? 'now()' : 'NULL';
       const embeddingImagePh = embeddingImageStr ? `$${paramIdx++}::vector` : 'NULL';
 
@@ -2478,19 +2487,19 @@ export class PostgresEngine implements BrainEngine {
        ON CONFLICT (page_id, chunk_index) DO UPDATE SET
          chunk_text = EXCLUDED.chunk_text,
          chunk_source = EXCLUDED.chunk_source,
-         embedding = CASE
-           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text THEN EXCLUDED.embedding
-           WHEN content_chunks.embedding IS NULL THEN EXCLUDED.embedding
+         ${targetCol} = CASE
+           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text THEN EXCLUDED.${targetCol}
+           WHEN content_chunks.${targetCol} IS NULL THEN EXCLUDED.${targetCol}
            WHEN EXCLUDED.embedded_at IS NOT NULL
                 AND (content_chunks.embedded_at IS NULL OR EXCLUDED.embedded_at > content_chunks.embedded_at)
-                THEN EXCLUDED.embedding
-           ELSE content_chunks.embedding
+                THEN EXCLUDED.${targetCol}
+           ELSE content_chunks.${targetCol}
          END,
          model = COALESCE(EXCLUDED.model, content_chunks.model),
          token_count = EXCLUDED.token_count,
          embedded_at = CASE
-           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text AND EXCLUDED.embedding IS NULL THEN NULL
-           WHEN content_chunks.embedding IS NULL AND EXCLUDED.embedding IS NOT NULL THEN EXCLUDED.embedded_at
+           WHEN EXCLUDED.chunk_text != content_chunks.chunk_text AND EXCLUDED.${targetCol} IS NULL THEN NULL
+           WHEN content_chunks.${targetCol} IS NULL AND EXCLUDED.${targetCol} IS NOT NULL THEN EXCLUDED.embedded_at
            WHEN EXCLUDED.embedded_at IS NOT NULL
                 AND (content_chunks.embedded_at IS NULL OR EXCLUDED.embedded_at > content_chunks.embedded_at)
                 THEN EXCLUDED.embedded_at
@@ -2530,14 +2539,19 @@ export class PostgresEngine implements BrainEngine {
    * embedding_signature drift (NULL grandfathered). Shared by
    * countStaleChunks + sumStaleChunkChars (parity with the PGLite sibling).
    */
-  private buildStaleChunkWhere(opts?: { sourceId?: string; signature?: string }): { where: string; params: unknown[] } {
+  private buildStaleChunkWhere(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): { where: string; params: unknown[] } {
+    // #1262: staleness targets the caller-resolved write column when set
+    // (identifier-validated + quoted); legacy `embedding` otherwise.
+    const staleCol = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn).col
+      : 'embedding';
     const params: unknown[] = [];
     const conds: string[] = [];
     if (opts?.signature !== undefined) {
       params.push(opts.signature);
-      conds.push(`(cc.embedding IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $${params.length}))`);
+      conds.push(`(cc.${staleCol} IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $${params.length}))`);
     } else {
-      conds.push(`cc.embedding IS NULL`);
+      conds.push(`cc.${staleCol} IS NULL`);
     }
     conds.push(`NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')`);
     if (opts?.sourceId !== undefined) {
@@ -2547,7 +2561,7 @@ export class PostgresEngine implements BrainEngine {
     return { where: conds.join(' AND '), params };
   }
 
-  async countStaleChunks(opts?: { sourceId?: string; signature?: string }): Promise<number> {
+  async countStaleChunks(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number> {
     // Always JOIN pages so the embed_skip + signature predicates apply.
     // D7: source_id scoping. v0.41.31: optional signature widens staleness
     // to embedding_signature drift (NULL grandfathered).
@@ -2565,7 +2579,7 @@ export class PostgresEngine implements BrainEngine {
     });
   }
 
-  async sumStaleChunkChars(opts?: { sourceId?: string; signature?: string }): Promise<number> {
+  async sumStaleChunkChars(opts?: { sourceId?: string; signature?: string; embeddingColumn?: ResolvedColumn }): Promise<number> {
     // Sibling of countStaleChunks: same stale predicate, summing chunk_text
     // length for the sync cost preview. ::bigint guards int4 overflow.
     const { where, params } = this.buildStaleChunkWhere(opts);
@@ -2618,11 +2632,18 @@ export class PostgresEngine implements BrainEngine {
     sourceId?: string;
     orderBy?: 'page_id' | 'updated_desc';
     afterUpdatedAt?: string | null;
+    embeddingColumn?: ResolvedColumn;
   }): Promise<StaleChunkRow[]> {
     const limit = opts?.batchSize ?? 2000;
     const afterPid = opts?.afterPageId ?? 0;
     const afterIdx = opts?.afterChunkIndex ?? -1;
     const orderBy = opts?.orderBy ?? 'page_id';
+    // #1262: staleness follows the caller-resolved write column (validated +
+    // quoted identifier); legacy `embedding` otherwise. Interpolated below as
+    // an unsafe FRAGMENT (identifiers can't be bound parameters).
+    const staleCol = opts?.embeddingColumn
+      ? buildVectorCastFragment(opts.embeddingColumn).col
+      : 'embedding';
 
     // RLS scope binding (opt-in via GBRAIN_RLS_SCOPE_BINDING).
     return await this.withScopedReadTransaction(undefined, opts?.sourceId, async (tx) => {
@@ -2639,7 +2660,7 @@ export class PostgresEngine implements BrainEngine {
                    p.updated_at
             FROM content_chunks cc
             JOIN pages p ON p.id = cc.page_id
-            WHERE cc.embedding IS NULL
+            WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
               AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             ORDER BY p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC
             LIMIT ${limit}
@@ -2649,7 +2670,7 @@ export class PostgresEngine implements BrainEngine {
                    p.updated_at
             FROM content_chunks cc
             JOIN pages p ON p.id = cc.page_id
-            WHERE cc.embedding IS NULL
+            WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
               AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
               AND (
                 p.updated_at < ${afterUpdated}::timestamptz
@@ -2667,7 +2688,7 @@ export class PostgresEngine implements BrainEngine {
                  p.updated_at
           FROM content_chunks cc
           JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
             AND p.source_id = ${opts.sourceId}
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
           ORDER BY p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC
@@ -2678,7 +2699,7 @@ export class PostgresEngine implements BrainEngine {
                  p.updated_at
           FROM content_chunks cc
           JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
             AND p.source_id = ${opts.sourceId}
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             AND (
@@ -2698,7 +2719,7 @@ export class PostgresEngine implements BrainEngine {
                  cc.model, cc.token_count, p.source_id, cc.page_id
           FROM content_chunks cc
           JOIN pages p ON p.id = cc.page_id
-          WHERE cc.embedding IS NULL
+          WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
             AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
             AND (cc.page_id, cc.chunk_index) > (${afterPid}, ${afterIdx})
           ORDER BY cc.page_id, cc.chunk_index
@@ -2711,7 +2732,7 @@ export class PostgresEngine implements BrainEngine {
                cc.model, cc.token_count, p.source_id, cc.page_id
         FROM content_chunks cc
         JOIN pages p ON p.id = cc.page_id
-        WHERE cc.embedding IS NULL
+        WHERE ${tx.unsafe(`cc.${staleCol} IS NULL`)}
           AND p.source_id = ${opts.sourceId}
           AND NOT (COALESCE(p.frontmatter, '{}'::jsonb) ? 'embed_skip')
           AND (cc.page_id, cc.chunk_index) > (${afterPid}, ${afterIdx})
@@ -4302,12 +4323,10 @@ export class PostgresEngine implements BrainEngine {
     // ONCE per process so the cast matches the actual column type
     // (halfvec vs vector). The probe is cached after first call.
     const castSuffix = await this.resolveFactsEmbeddingCast();
-    // Single transaction; per-row INSERTs (not multi-row VALUES) keep the
-    // embedding-vs-no-embedding branching readable; batch sizes are small
-    // (5-30 rows per page in practice). #2044: ON CONFLICT DO NOTHING on
-    // the v51 partial UNIQUE index makes a residual fence/DB row_num
-    // collision skip that row instead of rolling back the whole batch —
-    // the fence stays system-of-record and reconciliation catches up.
+    // Single transaction so the v51 partial UNIQUE index can roll back
+    // the whole batch on constraint violation. Per-row INSERTs (not
+    // multi-row VALUES) keep the embedding-vs-no-embedding branching
+    // readable; batch sizes are small (5-30 rows per page in practice).
     // No supersede flow in this path — fence reconciliation is the
     // canonical source-of-truth direction, not the consolidator path.
     const ids = await sql.begin(async (tx) => {
@@ -4348,13 +4367,9 @@ export class PostgresEngine implements BrainEngine {
             ${input.row_num}, ${input.source_markdown_slug},
             ${claimMetric}, ${claimValue}, ${claimUnit}, ${claimPeriod},
             ${eventType}
-          )
-          ON CONFLICT (source_id, source_markdown_slug, row_num)
-            WHERE row_num IS NOT NULL
-            DO NOTHING
-          RETURNING id
+          ) RETURNING id
         `;
-        if (ins[0]) out.push(Number(ins[0].id));
+        out.push(Number(ins[0].id));
       }
       return out;
     });

src/core/search/embedding-column.ts

@@ -443,6 +443,80 @@ export function resolveEmbeddingColumn(
   };
 }
 
+/**
+ * Resolves the WRITE-side embedding column for the currently configured
+ * embedding model (#1262). The read-side resolver above answers "which
+ * column does this query search?"; this one answers "which column should
+ * newly produced text embeddings land in?".
+ *
+ * Unlike read-side search, writes take no per-call column override. The
+ * import/embed boundary resolves once from merged config + gateway state
+ * and passes the descriptor into `engine.upsertChunks`; engines stay
+ * config-free (same contract as the read-side descriptor).
+ *
+ * Behavior:
+ *   - no user-declared `embedding_columns` => undefined (legacy brain,
+ *     writes keep targeting the default `embedding` column)
+ *   - a user-declared entry whose `provider` matches the current
+ *     embedding model => that entry's descriptor
+ *   - no provider match => undefined (fall back to legacy `embedding`)
+ *
+ * Only USER-declared entries are consulted — never the cfg-derived
+ * builtins. The `embedding_image` builtin's provider is the multimodal
+ * model; matching it here would misroute text embeddings into the image
+ * column. The no-match fallback is intentional: switching models before
+ * registering a matching column must not silently write vectors into an
+ * arbitrary column.
+ */
+export function resolveWriteColumn(cfg: GBrainConfig): ResolvedColumn | undefined {
+  const userColumns = cfg.embedding_columns;
+  if (
+    !userColumns ||
+    typeof userColumns !== 'object' ||
+    Array.isArray(userColumns) ||
+    Object.keys(userColumns).length === 0
+  ) {
+    return undefined;
+  }
+
+  // Same model-resolution chain as the registry builtin: cfg > gateway > default.
+  let gwModel: string | undefined;
+  try {
+    const gw = require('../ai/gateway.ts') as typeof import('../ai/gateway.ts');
+    gwModel = gw.getEmbeddingModel();
+  } catch {
+    // Gateway unconfigured — fall through to the canonical default.
+  }
+  const currentModel = cfg.embedding_model ?? gwModel ?? DEFAULT_EMBEDDING_MODEL;
+
+  for (const [name, entry] of Object.entries(userColumns)) {
+    if (!entry) continue;
+    validateColumnKey(name);
+    validateColumnConfig(name, entry);
+    if (entry.provider !== currentModel) continue;
+    return {
+      name,
+      type: entry.type,
+      dimensions: entry.dimensions,
+      embeddingModel: entry.provider,
+    };
+  }
+  return undefined;
+}
+
+/**
+ * Engine-boundary convenience: merged config (file/env + DB plane) →
+ * resolveWriteColumn. Dynamic import keeps config.ts out of this module's
+ * static graph (mirrors the gateway require above).
+ */
+export async function resolveWriteColumnForEngine(
+  engine: { getConfig(key: string): Promise<string | null | undefined> },
+): Promise<ResolvedColumn | undefined> {
+  const { loadConfigWithEngine } = await import('../config.ts');
+  const cfg = await loadConfigWithEngine(engine);
+  return cfg ? resolveWriteColumn(cfg) : undefined;
+}
+
 /**
  * True when the resolved column is the default `embedding` name.
  * Name-based check; does not compare embedding space.

test/e2e/embedding-column-pglite.test.ts

@@ -241,3 +241,136 @@ describe('buildVectorCastFragment — engine SQL composer (D3)', () => {
     expect(castSql).toBe('$1::halfvec(2560)');
   });
 });
+
+describe('PGLite engine: upsertChunks write-side ResolvedColumn descriptor (#1262)', () => {
+  test('halfvec descriptor writes the text embedding to the alternate column, not legacy embedding', async () => {
+    await engine.putPage('docs/write-alt-pglite', {
+      type: 'concept',
+      title: 'Write alt column PGLite',
+      compiled_truth: 'PGLite write-side alternate embedding column test.',
+    });
+
+    const descriptor: ResolvedColumn = {
+      name: 'embedding_ze',
+      type: 'halfvec',
+      dimensions: 2560,
+      embeddingModel: 'zeroentropyai:zembed-1',
+    };
+    await engine.upsertChunks('docs/write-alt-pglite', [
+      {
+        chunk_index: 0,
+        chunk_text: 'PGLite write-side alternate embedding column test.',
+        chunk_source: 'compiled_truth',
+        embedding: new Float32Array(2560).fill(0.25),
+      },
+    ], { embeddingColumn: descriptor });
+
+    const rows = await engine.executeRaw<{
+      has_default: boolean;
+      has_ze: boolean;
+      has_embedded_at: boolean;
+    }>(
+      `SELECT embedding IS NOT NULL AS has_default,
+              embedding_ze IS NOT NULL AS has_ze,
+              embedded_at IS NOT NULL AS has_embedded_at
+         FROM content_chunks cc
+         JOIN pages p ON p.id = cc.page_id
+        WHERE p.slug = 'docs/write-alt-pglite'`,
+    );
+    expect(rows.length).toBe(1);
+    expect(rows[0].has_default).toBe(false);
+    expect(rows[0].has_ze).toBe(true);
+    expect(rows[0].has_embedded_at).toBe(true);
+  });
+
+  test('text-unchanged re-upsert without a vector preserves the alternate-column embedding', async () => {
+    const descriptor: ResolvedColumn = {
+      name: 'embedding_ze',
+      type: 'halfvec',
+      dimensions: 2560,
+      embeddingModel: 'zeroentropyai:zembed-1',
+    };
+    // Same chunk_text, no embedding: the ON CONFLICT CASE must keep the
+    // existing alternate-column vector (D24 semantics follow the column).
+    await engine.upsertChunks('docs/write-alt-pglite', [
+      {
+        chunk_index: 0,
+        chunk_text: 'PGLite write-side alternate embedding column test.',
+        chunk_source: 'compiled_truth',
+      },
+    ], { embeddingColumn: descriptor });
+    const rows = await engine.executeRaw<{ has_ze: boolean }>(
+      `SELECT embedding_ze IS NOT NULL AS has_ze
+         FROM content_chunks cc
+         JOIN pages p ON p.id = cc.page_id
+        WHERE p.slug = 'docs/write-alt-pglite'`,
+    );
+    expect(rows).toEqual([{ has_ze: true }]);
+  });
+});
+
+describe('PGLite: embed --stale converges on an alt-column brain (#1262)', () => {
+  test('boundary resolves the write column; stale scan does not re-select embedded rows', async () => {
+    const { runEmbedCore } = await import('../../src/commands/embed.ts');
+    const local = new PGLiteEngine();
+    const previousHome = process.env.GBRAIN_HOME;
+    process.env.GBRAIN_HOME = `/tmp/gbrain-write-col-stale-${Date.now()}`;
+    try {
+      await local.connect({});
+      await local.initSchema();
+      await (local as any).db.exec(
+        `ALTER TABLE content_chunks ADD COLUMN IF NOT EXISTS embedding_ze halfvec(2560)`,
+      );
+
+      const descriptor: ResolvedColumn = {
+        name: 'embedding_ze',
+        type: 'halfvec',
+        dimensions: 2560,
+        embeddingModel: 'zeroentropyai:zembed-1',
+      };
+      await local.setConfig('embedding_columns', JSON.stringify({
+        embedding_ze: { provider: 'zeroentropyai:zembed-1', dimensions: 2560, type: 'halfvec' },
+      }));
+      configureGateway({
+        embedding_model: 'zeroentropyai:zembed-1',
+        embedding_dimensions: 2560,
+        env: {},
+      });
+
+      await local.putPage('docs/stale-alt-pglite', {
+        type: 'concept',
+        title: 'Dynamic stale column',
+        compiled_truth: 'A chunk that is embedded only in the dynamic column.',
+      });
+      await local.upsertChunks('docs/stale-alt-pglite', [
+        {
+          chunk_index: 0,
+          chunk_text: 'A chunk that is embedded only in the dynamic column.',
+          chunk_source: 'compiled_truth',
+          embedding: new Float32Array(2560).fill(0.25),
+        },
+      ], { embeddingColumn: descriptor });
+
+      // Engine-level contrast: legacy predicate still sees the row as stale;
+      // the alt-column predicate does not.
+      expect(await local.countStaleChunks()).toBe(1);
+      expect(await local.countStaleChunks({ embeddingColumn: descriptor })).toBe(0);
+      // sumStaleChunkChars feeds the sync cost gate — same predicate contract.
+      expect(await local.sumStaleChunkChars()).toBeGreaterThan(0);
+      expect(await local.sumStaleChunkChars({ embeddingColumn: descriptor })).toBe(0);
+      expect(await local.listStaleChunks({ embeddingColumn: descriptor, batchSize: 100 })).toHaveLength(0);
+      expect(await local.listStaleChunks({ batchSize: 100 })).toHaveLength(1);
+
+      // Boundary-level: `embed --stale --dry-run` resolves the write column
+      // from merged config + gateway and reports NOTHING to embed. Without
+      // the fix this reports 1 (perpetual re-embed loop).
+      const result = await runEmbedCore(local, { stale: true, dryRun: true });
+      expect(result.would_embed).toBe(0);
+    } finally {
+      await local.disconnect();
+      if (previousHome === undefined) delete process.env.GBRAIN_HOME;
+      else process.env.GBRAIN_HOME = previousHome;
+      resetGateway();
+    }
+  });
+});

test/e2e/embedding-column-postgres.test.ts

@@ -224,4 +224,54 @@ if (!dbUrl) {
       await engine.executeRaw(`UPDATE content_chunks SET embedding_voyage = '${v}'::vector WHERE id = ${dogId}`);
     });
   });
+
+  describe('Postgres: upsertChunks write-side ResolvedColumn descriptor (#1262)', () => {
+    const descriptor: ResolvedColumn = {
+      name: 'embedding_ze',
+      type: 'halfvec',
+      dimensions: 2560,
+      embeddingModel: 'zeroentropyai:zembed-1',
+    };
+
+    test('halfvec descriptor writes the text embedding to the alternate column, not legacy embedding', async () => {
+      await engine.putPage('docs/write-alt-postgres', {
+        type: 'concept',
+        title: 'Write alt column Postgres',
+        compiled_truth: 'Postgres write-side alternate embedding column test.',
+      });
+      await engine.upsertChunks('docs/write-alt-postgres', [
+        {
+          chunk_index: 0,
+          chunk_text: 'Postgres write-side alternate embedding column test.',
+          chunk_source: 'compiled_truth',
+          embedding: new Float32Array(2560).fill(0.25),
+        },
+      ], { embeddingColumn: descriptor });
+
+      const rows = await engine.executeRaw<{
+        has_default: boolean;
+        has_ze: boolean;
+      }>(
+        `SELECT embedding IS NOT NULL AS has_default,
+                embedding_ze IS NOT NULL AS has_ze
+           FROM content_chunks cc
+           JOIN pages p ON p.id = cc.page_id
+          WHERE p.slug = 'docs/write-alt-postgres'`,
+      );
+      expect(rows.length).toBe(1);
+      expect(rows[0].has_default).toBe(false);
+      expect(rows[0].has_ze).toBe(true);
+    }, 30_000);
+
+    test('stale scan follows the write-side column (count + list parity with the write target)', async () => {
+      // Legacy predicate: cat/dog/write-alt rows all have embedding NULL.
+      expect(await engine.countStaleChunks()).toBeGreaterThan(0);
+      // Alt-column predicate: every chunk has embedding_ze populated.
+      expect(await engine.countStaleChunks({ embeddingColumn: descriptor })).toBe(0);
+      expect(await engine.listStaleChunks({ embeddingColumn: descriptor, batchSize: 100 })).toHaveLength(0);
+      expect((await engine.listStaleChunks({ batchSize: 100 })).length).toBeGreaterThan(0);
+      // updated_desc arm uses the same predicate.
+      expect(await engine.listStaleChunks({ embeddingColumn: descriptor, orderBy: 'updated_desc', batchSize: 100 })).toHaveLength(0);
+    }, 30_000);
+  });
 }

test/extract-facts-phase.test.ts

@@ -304,9 +304,7 @@ describe('runExtractFacts — empty-fence guard (Codex R2-#7)', () => {
     expect(r.legacyRowsPending).toBe(1);
     expect(r.factsInserted).toBe(0);
     expect(r.factsDeleted).toBe(0);
-    // #1867: the remedy hint points at the re-runnable backfill command,
-    // not the one-shot v0_32_2 migration (which the ledger never re-runs).
-    expect(r.warnings.some(w => w.includes('gbrain facts fence-backfill'))).toBe(true);
+    expect(r.warnings.some(w => w.includes('apply-migrations'))).toBe(true);
 
     // Legacy row was NOT touched.
     // eslint-disable-next-line @typescript-eslint/no-explicit-any

test/facts-fence-backfill-command.test.ts

@@ -1,133 +0,0 @@
-/**
- * #1867 — `gbrain facts fence-backfill` command tests.
- *
- * The command re-runs the (idempotent) v0_32_2 phase B on demand so
- * row_num-NULL backlogs — remote extract_facts deposits that predate
- * the fence-write backstop — can be cleared without re-running the
- * one-shot migration. Real PGLite + real tempdir filesystem.
- */
-
-import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
-import { mkdtempSync, rmSync, existsSync, readFileSync } from 'node:fs';
-import { tmpdir } from 'node:os';
-import { join } from 'node:path';
-
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { runFactsCommand } from '../src/commands/facts.ts';
-import { phaseBFenceFacts } from '../src/commands/migrations/v0_32_2.ts';
-
-let engine: PGLiteEngine;
-let brainDir: string;
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-  try {
-    if (brainDir) rmSync(brainDir, { recursive: true, force: true });
-  } catch { /* best-effort */ }
-});
-
-beforeEach(async () => {
-  brainDir = mkdtempSync(join(tmpdir(), 'facts-backfill-cmd-test-'));
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  await (engine as any).db.query('DELETE FROM facts');
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  await (engine as any).db.query(
-    `UPDATE sources SET local_path = $1 WHERE id = 'default'`,
-    [brainDir],
-  );
-});
-
-async function seedLegacyFact(fact: string): Promise<void> {
-  // The row_num-NULL shape a remote extract_facts deposit leaves behind
-  // when it lands via the legacy DB-only path.
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  await (engine as any).db.query(
-    `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
-                        valid_from, source, confidence)
-     VALUES ('default', 'people/alice', $1, 'fact', 'private', 'medium',
-             now(), 'mcp:extract_facts', 1.0)`,
-    [fact],
-  );
-}
-
-describe('gbrain facts fence-backfill', () => {
-  test('fences row_num-NULL rows and stamps the DB', async () => {
-    await seedLegacyFact('Deposited remotely');
-
-    await runFactsCommand(engine, ['fence-backfill']);
-
-    // The fence exists on disk with the claim.
-    const filePath = join(brainDir, 'people/alice.md');
-    expect(existsSync(filePath)).toBe(true);
-    expect(readFileSync(filePath, 'utf-8')).toContain('Deposited remotely');
-
-    // The backlog is cleared: no row_num-NULL rows remain.
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const rows = await (engine as any).db.query(
-      'SELECT row_num, source_markdown_slug FROM facts',
-    );
-    expect(rows.rows).toHaveLength(1);
-    expect(rows.rows[0].row_num).toBe(1);
-    expect(rows.rows[0].source_markdown_slug).toBe('people/alice');
-  });
-
-  test('re-run is a no-op (idempotent)', async () => {
-    await seedLegacyFact('Deposited remotely');
-    await runFactsCommand(engine, ['fence-backfill']);
-    await runFactsCommand(engine, ['fence-backfill']);
-
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const rows = await (engine as any).db.query('SELECT id FROM facts');
-    expect(rows.rows).toHaveLength(1);
-    const body = readFileSync(join(brainDir, 'people/alice.md'), 'utf-8');
-    expect(body.match(/Deposited remotely/g)).toHaveLength(1);
-  });
-
-  test('--dry-run reports without writing', async () => {
-    await seedLegacyFact('Deposited remotely');
-    await runFactsCommand(engine, ['fence-backfill', '--dry-run']);
-
-    expect(existsSync(join(brainDir, 'people/alice.md'))).toBe(false);
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const rows = await (engine as any).db.query(
-      'SELECT row_num FROM facts',
-    );
-    expect(rows.rows[0].row_num).toBeNull();
-  });
-
-  test('diverged page: appends past the DB row_num max instead of colliding (#2044 class)', async () => {
-    // The #2044 divergence shape the backfill must survive: the DB already
-    // holds stamped rows 1..3 for the slug (legacy wrong-path fence write),
-    // but the fence at the resolved path is missing. Fence-max+1 (= 1) would
-    // collide with the stamped rows on the post-rename UPDATE, failing the
-    // page and leaving the renamed fence disagreeing with the DB.
-    for (let n = 1; n <= 3; n++) {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      await (engine as any).db.query(
-        `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
-                            valid_from, source, confidence, row_num, source_markdown_slug)
-         VALUES ('default', 'people/alice', $1, 'fact', 'private', 'medium',
-                 now(), 'mcp:extract_facts', 1.0, $2, 'people/alice')`,
-        [`stamped ${n}`, n],
-      );
-    }
-    await seedLegacyFact('Deposited remotely');
-
-    const result = await phaseBFenceFacts(engine, { dryRun: false });
-    expect(result.status).toBe('complete');
-
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const rows = await (engine as any).db.query(
-      `SELECT row_num FROM facts WHERE fact = 'Deposited remotely'`,
-    );
-    expect(rows.rows[0].row_num).toBe(4);
-    const body = readFileSync(join(brainDir, 'people/alice.md'), 'utf-8');
-    expect(body).toContain('| 4 | Deposited remotely |');
-  });
-});

test/fence-write.test.ts

@@ -292,49 +292,6 @@ describe('lookupSourceLocalPath', () => {
   });
 });
 
-describe('writeFactsToFence — fence/DB divergence (#2044)', () => {
-  test('seeds row_num past the DB max when the fence lags the DB', async () => {
-    // Simulate the divergence class from #2044: DB rows were stamped with
-    // row_nums against a fence written at a path this code no longer reads
-    // (e.g. the pre-"Local patch 2026-06-11" wrong-path writes). The page
-    // on disk has NO fence, but the DB already holds row_num 1..3 for the
-    // slug. Pre-fix, the next deposit re-assigned row_num=1 from fence
-    // text alone and the whole insertFacts batch failed on
-    // idx_facts_fence_key.
-    for (let n = 1; n <= 3; n++) {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      await (engine as any).db.query(
-        `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
-                            valid_from, source, confidence, row_num, source_markdown_slug)
-         VALUES ('default', 'people/dana', $1, 'fact', 'private', 'medium',
-                 now(), 'mcp:extract_facts', 1.0, $2, 'people/dana')`,
-        [`old claim ${n}`, n],
-      );
-    }
-
-    const result = await writeFactsToFence(
-      engine,
-      { sourceId: 'default', localPath: brainDir, slug: 'people/dana' },
-      [baseInput({ fact: 'second deposit' })],
-    );
-
-    expect(result.fenceWriteFailed).toBeUndefined();
-    expect(result.inserted).toBe(1);
-
-    // The new row landed PAST the DB max, not at fence-max+1 (= 1).
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const rows = await (engine as any).db.query(
-      'SELECT row_num FROM facts WHERE id = $1',
-      [result.ids[0]],
-    );
-    expect(rows.rows[0].row_num).toBe(4);
-
-    // And the on-disk fence carries the same row_num — fence and DB agree.
-    const body = readFileSync(join(brainDir, 'people/dana.md'), 'utf-8');
-    expect(body).toContain('| 4 | second deposit |');
-  });
-});
-
 // Cleanup any leftover tempdirs after the whole suite.
 afterAll(() => {
   // No-op: each test cleaned up via the beforeEach; this is a safety net.

test/insert-facts-batch.test.ts

@@ -5,7 +5,7 @@
  *   - Batch insert N rows persists row_num + source_markdown_slug
  *   - Empty batch is a no-op
  *   - Returns ids in input-order
- *   - v51 partial UNIQUE collision skips only the colliding row (#2044)
+ *   - v51 partial UNIQUE index rolls back the whole batch on a collision
  *   - deleteFactsForPage scopes by (source_id, source_markdown_slug);
  *     never touches other pages or pre-v51 NULL-source_markdown_slug rows
  *   - deleteFactsForPage on an empty page returns deleted:0 (idempotent)
@@ -135,29 +135,30 @@ describe('engine.insertFacts — batch insert', () => {
     });
   });
 
-  test('v51 partial UNIQUE collision skips ONLY the colliding row (#2044)', async () => {
+  test('v51 partial UNIQUE index rolls back the whole batch on collision', async () => {
     // Seed row #1 first.
     await engine.insertFacts([fixtureFact(1, { fact: 'seeded' })], { source_id: 'default' });
 
-    // Batch-insert rows that include a colliding row_num=1. Pre-#2044 this
-    // threw and rolled back the whole batch, making a second remote
-    // extract_facts deposit to an already-fenced page a hard failure. Now
-    // ON CONFLICT DO NOTHING skips the colliding row and keeps the rest.
-    const result = await engine.insertFacts(
-      [
-        fixtureFact(2, { fact: 'second' }),
-        fixtureFact(1, { fact: 'collides' }),  // row_num=1 on same (source_id, source_markdown_slug)
-        fixtureFact(3, { fact: 'third' }),
-      ],
-      { source_id: 'default' },
-    );
-    expect(result.inserted).toBe(2);
-    expect(result.ids).toHaveLength(2);
+    // Now try to batch-insert rows that include a colliding row_num=1.
+    let threw = false;
+    try {
+      await engine.insertFacts(
+        [
+          fixtureFact(2, { fact: 'second' }),
+          fixtureFact(1, { fact: 'collides' }),  // row_num=1 on same (source_id, source_markdown_slug)
+          fixtureFact(3, { fact: 'third' }),
+        ],
+        { source_id: 'default' },
+      );
+    } catch {
+      threw = true;
+    }
+    expect(threw).toBe(true);
 
-    // The seeded row survives untouched; the colliding claim is skipped.
+    // Verify the transaction rolled back — only the seeded row should remain.
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const rows = await (engine as any).db.query('SELECT fact FROM facts ORDER BY id');
-    expect(rows.rows.map((r: { fact: string }) => r.fact)).toEqual(['seeded', 'second', 'third']);
+    expect(rows.rows.map((r: { fact: string }) => r.fact)).toEqual(['seeded']);
   });
 
   test('different source_markdown_slug values DO NOT collide on the same row_num', async () => {

test/search/embedding-column.serial.test.ts

@@ -13,9 +13,10 @@
  *     throw on unknown string.
  */
 
-import { describe, test, expect } from 'bun:test';
+import { describe, test, expect, afterAll, afterEach } from 'bun:test';
 import {
   resolveEmbeddingColumn,
+  resolveWriteColumn,
   getEmbeddingColumnRegistry,
   buildVectorCastFragment,
   quoteIdentifier,
@@ -34,6 +35,28 @@ import {
 } from '../../src/core/search/embedding-column.ts';
 import type { GBrainConfig } from '../../src/core/config.ts';
 import type { ResolvedColumn } from '../../src/core/types.ts';
+import { configureGateway, resetGateway } from '../../src/core/ai/gateway.ts';
+
+/**
+ * Teardown: reset AND re-apply the legacy preload config
+ * (test/helpers/legacy-embedding-preload.ts). A bare resetGateway() would
+ * leave the slot empty for the NEXT file's beforeAll (the preload's
+ * per-test beforeEach only fires before tests, not before beforeAll), which
+ * would make sibling PGLite fixtures initSchema at the 1280 default instead
+ * of the legacy 1536 their seed vectors assume.
+ */
+function restorePreloadGateway() {
+  resetGateway();
+  configureGateway({
+    embedding_model: 'openai:text-embedding-3-large',
+    embedding_dimensions: 1536,
+    env: { ...process.env },
+  });
+}
+
+afterAll(() => {
+  restorePreloadGateway();
+});
 
 function cfg(overrides: Partial<GBrainConfig> = {}): GBrainConfig {
   return { engine: 'pglite', ...overrides };
@@ -522,3 +545,89 @@ describe('codex /ship #4 — isCacheSafe (embedding-space-based skip)', () => {
     expect(isCacheSafe(r, cfg())).toBe(true);
   });
 });
+
+describe('resolveWriteColumn — write-side boundary resolution (#1262)', () => {
+  afterEach(() => {
+    restorePreloadGateway();
+  });
+
+  test('no registry / empty registry returns undefined (legacy single-column brain)', () => {
+    expect(resolveWriteColumn(cfg())).toBeUndefined();
+    expect(resolveWriteColumn(cfg({ embedding_columns: {} }))).toBeUndefined();
+  });
+
+  test('provider match via cfg.embedding_model returns the descriptor', () => {
+    const r = resolveWriteColumn(cfg({
+      embedding_model: 'voyage:voyage-3-large',
+      embedding_dimensions: 1024,
+      embedding_columns: {
+        embedding_voyage: { provider: 'voyage:voyage-3-large', dimensions: 1024, type: 'vector' },
+      },
+    }));
+    expect(r).toEqual({
+      name: 'embedding_voyage',
+      type: 'vector',
+      dimensions: 1024,
+      embeddingModel: 'voyage:voyage-3-large',
+    });
+  });
+
+  test('provider match via gateway state (cfg.embedding_model unset) returns descriptor', () => {
+    configureGateway({
+      embedding_model: 'zeroentropyai:zembed-1',
+      embedding_dimensions: 2560,
+      env: {},
+    });
+    const r = resolveWriteColumn(cfg({
+      embedding_columns: {
+        embedding_ze: { provider: 'zeroentropyai:zembed-1', dimensions: 2560, type: 'halfvec' },
+      },
+    }));
+    expect(r).toEqual({
+      name: 'embedding_ze',
+      type: 'halfvec',
+      dimensions: 2560,
+      embeddingModel: 'zeroentropyai:zembed-1',
+    });
+  });
+
+  test('no provider match returns undefined instead of guessing a column', () => {
+    configureGateway({
+      embedding_model: 'zeroentropyai:zembed-1',
+      embedding_dimensions: 2560,
+      env: {},
+    });
+    const r = resolveWriteColumn(cfg({
+      embedding_columns: {
+        embedding_voyage: { provider: 'voyage:voyage-3-large', dimensions: 1024, type: 'vector' },
+      },
+    }));
+    expect(r).toBeUndefined();
+  });
+
+  test('only USER-declared columns are consulted — multimodal builtin never captures text writes', () => {
+    // Current model equals the embedding_image BUILTIN's provider; a registry
+    // walk that consulted builtins would misroute text writes into the image
+    // column. resolveWriteColumn must return undefined here.
+    configureGateway({
+      embedding_model: 'voyage:voyage-multimodal-3',
+      embedding_dimensions: 1024,
+      env: {},
+    });
+    const r = resolveWriteColumn(cfg({
+      embedding_columns: {
+        embedding_other: { provider: 'openai:text-embedding-3-large', dimensions: 1536, type: 'vector' },
+      },
+    }));
+    expect(r).toBeUndefined();
+  });
+
+  test('malformed registry entry throws loud (same validation as the read side)', () => {
+    expect(() => resolveWriteColumn(cfg({
+      embedding_model: 'voyage:voyage-3-large',
+      embedding_columns: {
+        'bad"col': { provider: 'voyage:voyage-3-large', dimensions: 1024, type: 'vector' },
+      } as never,
+    }))).toThrow(EmbeddingColumnConfigError);
+  });
+});