Archive every deletion via a bulk SQL retirement

`retireDeletedArtifacts` used to iterate `deleted.slice(0,
MAX_BASH_PROJECTED_FILES)` and emit no signal for paths past the cap
— a large `rm -r` would leave the 51st row onward visible in the
DocumentCenter with no indication anything was missed. The cap was
inherited from the registration path, where it bounds file-stat
round-trips; retirement is a pure metadata update with no filesystem
cost, so the cap was value-free safety theatre.

New DB surface `archiveWorkProductsByExternalPaths` runs a single
`UPDATE … SET status = 'archived' … WHERE external_id IN (…)
AND status <> 'archived' RETURNING id, external_id` per 500-path
chunk — one round-trip per chunk instead of one per path. The
projector feeds the full `deleted` list in, maps the returned ids
back to `retired` outcomes, and no deletion is left behind regardless
of the run's cleanup fan-out size.

src/main/agent-runtime/artifact-projector.ts

@@ -312,6 +312,10 @@ function projectChangedPaths(
  * path. `last_touched_by_run_id` carries the retiring run so the
  * provenance timeline records the deletion alongside the earlier
  * edits.
+ *
+ * Every detected deletion is processed — retirement is a bulk
+ * `UPDATE … IN (…)` chunked by the DB layer, so a large `rm -r`
+ * retires the full tail instead of leaving the overflow visible.
  */
 function retireDeletedArtifacts(
   db: AppDatabase,
@@ -319,24 +323,18 @@ function retireDeletedArtifacts(
   deleted: string[],
 ): ProjectionOutcome[] {
   if (deleted.length === 0) return [];
-  const outcomes: ProjectionOutcome[] = [];
-  const budget = deleted.slice(0, MAX_BASH_PROJECTED_FILES);
-  for (const rel of budget) {
-    const existing = db.findWorkProductByExternalId(
-      ctx.companyId,
-      "filesystem",
-      rel,
-      ctx.workspaceId,
-    );
-    if (!existing) continue;
-    db.updateWorkProduct(existing.id, ctx.companyId, {
-      status: "archived",
-      lastTouchedByRunId: ctx.runId,
-      workspaceId: ctx.workspaceId,
-    });
-    outcomes.push({ kind: "retired", workProductId: existing.id, relativePath: rel });
-  }
-  return outcomes;
+  const archived = db.archiveWorkProductsByExternalPaths({
+    companyId: ctx.companyId,
+    workspaceId: ctx.workspaceId,
+    provider: "filesystem",
+    paths: deleted,
+    lastTouchedByRunId: ctx.runId,
+  });
+  return archived.map(({ id, externalId }) => ({
+    kind: "retired",
+    workProductId: id,
+    relativePath: externalId,
+  }));
 }
 
 /**

src/main/database.ts

@@ -100,6 +100,9 @@ export class AppDatabase extends AppDatabaseBase {
   findWorkProductByExternalId(companyId: string, provider: string, externalId: string, workspaceId: string | null) { return this.documentsMod.findWorkProductByExternalId(companyId, provider, externalId, workspaceId); }
   resolveWorkProductTarget(workProductId: string, companyId: string) { return this.documentsMod.resolveWorkProductTarget(workProductId, companyId); }
   deleteWorkProduct(id: string, companyId: string) { return this.documentsMod.deleteWorkProduct(id, companyId); }
+  archiveWorkProductsByExternalPaths(input: Parameters<ReturnType<typeof import("./database/documents").buildDocumentMethods>["archiveWorkProductsByExternalPaths"]>[0]) {
+    return this.documentsMod.archiveWorkProductsByExternalPaths(input);
+  }
   linkDocumentToTask(taskId: string, documentId: string, companyId: string, key: string) { return this.documentsMod.linkDocumentToTask(taskId, documentId, companyId, key); }
   unlinkDocumentFromTask(taskId: string, key: string, companyId: string) { this.documentsMod.unlinkDocumentFromTask(taskId, key, companyId); }
   listDocumentsForTask(taskId: string, companyId: string) { return this.documentsMod.listDocumentsForTask(taskId, companyId); }

src/main/database/documents.ts

@@ -451,6 +451,65 @@ export function buildDocumentMethods(
       return Number(result.changes ?? 0);
     },
 
+    /**
+     * Archive every `work_products` row whose natural identity matches
+     * one of `paths` under the given `(companyId, workspaceId,
+     * provider)` scope. The change detectors walk the whole workspace
+     * delta, so every detected deletion has to be retired — previously
+     * the projector capped the retire list at a hardcoded budget and
+     * the tail stayed visible in the DocumentCenter.
+     *
+     * Runs as a single `UPDATE … WHERE external_id IN (…)` per chunk
+     * so bulk deletions cost one SQL round-trip per 500 paths instead
+     * of one per path. `RETURNING` carries the archived row ids back
+     * to the projector so it can emit `retired` outcomes without a
+     * follow-up SELECT.
+     */
+    archiveWorkProductsByExternalPaths(input: {
+      companyId: string;
+      workspaceId: string | null;
+      provider: string;
+      paths: string[];
+      lastTouchedByRunId: string | null;
+    }): Array<{ id: string; externalId: string }> {
+      if (input.paths.length === 0) return [];
+      const ts = nowIso();
+      const CHUNK = 500;
+      const workspaceClause = input.workspaceId
+        ? "AND workspace_id = ?"
+        : "AND workspace_id IS NULL";
+      const results: Array<{ id: string; externalId: string }> = [];
+      for (let i = 0; i < input.paths.length; i += CHUNK) {
+        const chunk = input.paths.slice(i, i + CHUNK);
+        const placeholders = chunk.map(() => "?").join(", ");
+        const params: SQLInputValue[] = [
+          input.lastTouchedByRunId ?? null,
+          ts,
+          input.companyId,
+          input.provider,
+        ];
+        if (input.workspaceId) params.push(input.workspaceId);
+        params.push(...chunk);
+        const rows = readAll<{ id: string; external_id: string }>(
+          `UPDATE work_products
+              SET status = 'archived',
+                  last_touched_by_run_id = ?,
+                  updated_at = ?
+            WHERE company_id = ?
+              AND provider = ?
+              ${workspaceClause}
+              AND external_id IN (${placeholders})
+              AND status <> 'archived'
+          RETURNING id, external_id`,
+          ...params,
+        );
+        for (const row of rows) {
+          results.push({ id: row.id, externalId: row.external_id });
+        }
+      }
+      return results;
+    },
+
     // ── Task-Document Links ──
 
     linkDocumentToTask(taskId: string, documentId: string, companyId: string, key: string): string {