feat(server): impl doc gc (#15282)

#### PR Dependency Tree


* **PR #15282** 👈

This tree was auto-generated by
[Charcoal](https://github.com/danerwilliams/charcoal)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Added automated document cleanup to reconcile missing workspace docs,
delete related stored data, and recover if the doc returns.
* Added effect-based follow-up reconciliation for search indexing,
Copilot embeddings, and comment attachment cleanup with explicit
acknowledgements.
* **Bug Fixes**
* Deleted-document references now persist as dangling references rather
than disappearing.
* Improved document deletion flow to enforce permissions and ensure
authorized deletions succeed.
* **Tests**
* Expanded coverage for cleanup recovery, indexing/embedding
reconciliation, permissions, and reference semantics.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

blocksuite/integration-test/src/__tests__/main/editor-semantics.spec.ts

@@ -1,5 +1,6 @@
 import { LinkExtension } from '@blocksuite/affine-inline-link';
 import { textKeymap } from '@blocksuite/affine-inline-preset';
+import type { AffineReference } from '@blocksuite/affine-inline-reference';
 import type {
   ListBlockModel,
   ParagraphBlockModel,
@@ -312,6 +313,16 @@ describe('hotkey/bracket/linked-page', () => {
     const richText = getRichTextByBlockId(paragraphId);
     expect(richText.querySelectorAll('affine-reference').length).toBe(2);
     expect(richText.inlineEditor.yTextString.length).toBe(2);
+
+    collection.removeDoc(linkedDoc.id);
+    await wait();
+    expect(collection.docs.has(linkedDoc.id)).toBe(false);
+    const danglingReferences =
+      richText.querySelectorAll<AffineReference>('affine-reference');
+    expect(danglingReferences.length).toBe(2);
+    expect([...danglingReferences].every(reference => !reference.refMeta)).toBe(
+      true
+    );
   });
 });
 

packages/backend/native/index.d.ts

@@ -22,7 +22,6 @@ export declare class BackendRuntime {
   compactPendingDocUpdates(workspaceId: string, docId: string, batchLimit: number, historyMinIntervalMs: number, historyMaxAgeSeconds: number, owner: string, leaseTtlMs: number): Promise<RuntimeDocCompactionResult>
   upsertDocSnapshot(workspaceId: string, docId: string, blob: Buffer, timestampMs: number, editorId?: string | undefined | null): Promise<boolean>
   createDocHistory(input: RuntimeDocHistoryInput): Promise<boolean>
-  deleteDocStorage(workspaceId: string, docId: string): Promise<void>
   putRuntimeGateIfAbsent(key: string, ttlMs: number): Promise<boolean>
   cleanupExpiredRuntimeGates(limit: number): Promise<number>
   cleanupExpiredUserSessions(limit: number): Promise<number>
@@ -78,6 +77,9 @@ export declare class StorageRuntime {
   backfillMissingBlobMetadata(workspaceId: string | undefined | null, limit: number): Promise<RuntimeBlobMetadataBackfillResult>
   rebuildDocBlobRefs(workspaceId: string, docId: string): Promise<RuntimeDocBlobRefsResult>
   rebuildWorkspaceDocBlobRefs(workspaceId: string, limit: number): Promise<RuntimeDocBlobRefsResult>
+  reconcileWorkspaceDocuments(workspaceId: string): Promise<RuntimeDocumentCleanupReconcileResult>
+  executeDocumentCleanupCandidates(workspaceId: string | undefined | null, gracePeriodDays: number, limit: number): Promise<RuntimeDocumentCleanupExecuteResult>
+  ackDocumentCleanupEffect(workspaceId: string, docId: string, cleanupVersion: string, effect: string): Promise<RuntimeDocumentCleanupAckResult>
   constructor()
   start(): Promise<void>
   configure(configJson: string): void
@@ -976,6 +978,37 @@ export interface RuntimeDocHistoryInput {
   historyMaxAgeMs: number
 }
 
+export interface RuntimeDocumentCleanupAckResult {
+  completed: boolean
+}
+
+export interface RuntimeDocumentCleanupEffect {
+  workspaceId: string
+  docId: string
+  cleanupVersion: string
+  commentObjectsDone: boolean
+  searchDone: boolean
+  copilotDone: boolean
+}
+
+export interface RuntimeDocumentCleanupExecuteResult {
+  scannedCandidates: number
+  serializationRetries: number
+  executed: number
+  recovered: number
+  reset: number
+  failed: number
+  deletedRows: number
+  effects: Array<RuntimeDocumentCleanupEffect>
+}
+
+export interface RuntimeDocumentCleanupReconcileResult {
+  scannedDocs: number
+  marked: number
+  reset: number
+  recovered: number
+}
+
 export interface RuntimeInviteAbuseActionRequired {
   action: string
   subjectKey: string

packages/backend/native/src/runtime/backend_runtime/doc_storage.rs

@@ -126,37 +126,4 @@ impl BackendRuntime {
 
     Ok(true)
   }
-
-  #[napi]
-  pub async fn delete_doc_storage(&self, workspace_id: String, doc_id: String) -> napi::Result<()> {
-    let pool = self.pool().await?;
-    let mut tx = pool
-      .begin()
-      .await
-      .map_err(|err| RuntimeError::database("DocStorage delete begin transaction failed", err))?;
-
-    sqlx::query("DELETE FROM snapshots WHERE workspace_id = $1 AND guid = $2")
-      .bind(&workspace_id)
-      .bind(&doc_id)
-      .execute(&mut *tx)
-      .await
-      .map_err(|err| RuntimeError::database("DocStorage delete snapshot failed", err))?;
-    sqlx::query("DELETE FROM updates WHERE workspace_id = $1 AND guid = $2")
-      .bind(&workspace_id)
-      .bind(&doc_id)
-      .execute(&mut *tx)
-      .await
-      .map_err(|err| RuntimeError::database("DocStorage delete updates failed", err))?;
-    sqlx::query("DELETE FROM snapshot_histories WHERE workspace_id = $1 AND guid = $2")
-      .bind(&workspace_id)
-      .bind(&doc_id)
-      .execute(&mut *tx)
-      .await
-      .map_err(|err| RuntimeError::database("DocStorage delete histories failed", err))?;
-
-    tx.commit()
-      .await
-      .map_err(|err| RuntimeError::database("DocStorage delete commit failed", err))?;
-    Ok(())
-  }
 }

packages/backend/native/src/runtime/backend_runtime/tests.rs

@@ -18,8 +18,9 @@ fn migrations_include_runtime_tables_without_worker_heartbeats() {
   assert!(RUNTIME_MIGRATIONS.contains("runtime_states"));
   assert!(RUNTIME_MIGRATIONS.contains("runtime_gates"));
   assert!(RUNTIME_MIGRATIONS.contains("runtime_leases"));
-  assert!(RUNTIME_MIGRATIONS.contains("blob_reconciliation_runs"));
+  assert!(RUNTIME_MIGRATIONS.contains("storage_reconciliation_runs"));
-  assert!(RUNTIME_MIGRATIONS.contains("blob_reconciliation_checkpoints"));
+  assert!(RUNTIME_MIGRATIONS.contains("storage_reconciliation_checkpoints"));
+  assert!(RUNTIME_MIGRATIONS.contains("document_cleanup_candidates"));
   assert!(RUNTIME_MIGRATIONS.contains("doc_blob_refs"));
   assert!(RUNTIME_MIGRATIONS.contains("blob_cleanup_candidates"));
   assert!(!RUNTIME_MIGRATIONS.contains("runtime_worker_heartbeats"));
@@ -136,12 +137,10 @@ async fn insert_invite_quota_fixture(
   .bind(email)
   .execute(&pool)
   .await?;
-  sqlx::query(
+  sqlx::query("INSERT INTO workspaces (id, created_at) VALUES ($1, clock_timestamp() - interval '60 days')")
-    "INSERT INTO workspaces (id, public, created_at) VALUES ($1, false, clock_timestamp() - interval '60 days')",
+    .bind(&workspace_id)
-  )
+    .execute(&pool)
-  .bind(&workspace_id)
+    .await?;
-  .execute(&pool)
-  .await?;
   sqlx::query(
     r#"
     INSERT INTO effective_workspace_quota_states (

packages/backend/native/src/runtime/error.rs

@@ -97,6 +97,16 @@ impl RuntimeError {
       _ => false,
     }
   }
+
+  pub(crate) fn is_serialization_failure(&self) -> bool {
+    matches!(
+      self,
+      Self::Database {
+        source: sqlx::Error::Database(source),
+        ..
+      } if source.code().as_deref() == Some("40001")
+    )
+  }
 }
 
 pub(crate) fn to_napi_error(error: RuntimeError) -> Error {

packages/backend/native/src/runtime/migrations.rs

@@ -5,16 +5,10 @@ use super::{RuntimeError, RuntimeResult};
 pub(crate) const RUNTIME_MIGRATIONS: &str = include_str!("sql/runtime_migrations.sql");
 
 pub(crate) async fn migrate_runtime_tables(pool: &PgPool) -> RuntimeResult<()> {
-  for statement in RUNTIME_MIGRATIONS
+  sqlx::raw_sql(RUNTIME_MIGRATIONS)
-    .split(';')
+    .execute(pool)
-    .map(str::trim)
+    .await
-    .filter(|statement| !statement.is_empty())
+    .map_err(|err| RuntimeError::database("Runtime migration failed", err))?;
-  {
-    sqlx::query(statement)
-      .execute(pool)
-      .await
-      .map_err(|err| RuntimeError::database("Runtime migration failed", err))?;
-  }
 
   Ok(())
 }

packages/backend/native/src/runtime/sql/runtime_migrations.sql

@@ -39,7 +39,7 @@ CREATE TABLE IF NOT EXISTS runtime_leases (
 CREATE INDEX IF NOT EXISTS runtime_leases_expires_at_idx
   ON runtime_leases (expires_at);
 
-CREATE TABLE IF NOT EXISTS blob_reconciliation_runs (
+CREATE TABLE IF NOT EXISTS storage_reconciliation_runs (
   id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
   kind TEXT NOT NULL,
   mode TEXT NOT NULL,
@@ -54,10 +54,10 @@ CREATE TABLE IF NOT EXISTS blob_reconciliation_runs (
   metadata JSONB NOT NULL DEFAULT '{}'
 );
 
-CREATE INDEX IF NOT EXISTS blob_reconciliation_runs_workspace_idx
+CREATE INDEX IF NOT EXISTS storage_reconciliation_runs_workspace_idx
-  ON blob_reconciliation_runs (workspace_id, started_at DESC);
+  ON storage_reconciliation_runs (workspace_id, started_at DESC);
 
-CREATE TABLE IF NOT EXISTS blob_reconciliation_checkpoints (
+CREATE TABLE IF NOT EXISTS storage_reconciliation_checkpoints (
   kind TEXT NOT NULL,
   scope TEXT NOT NULL,
   status TEXT NOT NULL,
@@ -70,8 +70,28 @@ CREATE TABLE IF NOT EXISTS blob_reconciliation_checkpoints (
   PRIMARY KEY (kind, scope)
 );
 
-CREATE INDEX IF NOT EXISTS blob_reconciliation_checkpoints_status_idx
+CREATE INDEX IF NOT EXISTS storage_reconciliation_checkpoints_status_idx
-  ON blob_reconciliation_checkpoints (kind, status, updated_at DESC);
+  ON storage_reconciliation_checkpoints (kind, status, updated_at DESC);
+
+CREATE TABLE IF NOT EXISTS document_cleanup_candidates (
+  workspace_id TEXT NOT NULL,
+  doc_id TEXT NOT NULL,
+  status TEXT NOT NULL CHECK (status IN ('marked', 'effects_pending', 'failed')),
+  missing_since TIMESTAMPTZ(3) NOT NULL,
+  last_observed_missing_at TIMESTAMPTZ(3) NOT NULL,
+  last_doc_activity_at TIMESTAMPTZ(3),
+  cleanup_payload JSONB NOT NULL DEFAULT '{}',
+  attempt_count INTEGER NOT NULL DEFAULT 0 CHECK (attempt_count >= 0),
+  error TEXT,
+  updated_at TIMESTAMPTZ(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (workspace_id, doc_id)
+);
+
+CREATE INDEX IF NOT EXISTS document_cleanup_candidates_status_missing_idx
+  ON document_cleanup_candidates (status, missing_since);
+
+CREATE INDEX IF NOT EXISTS document_cleanup_candidates_workspace_status_idx
+  ON document_cleanup_candidates (workspace_id, status, updated_at DESC);
 
 CREATE TABLE IF NOT EXISTS doc_blob_refs (
   workspace_id TEXT NOT NULL,

packages/backend/native/src/runtime/storage_runtime/blob_cleanup.rs

@@ -35,7 +35,7 @@ fn push_workspace_once(workspace_ids: &mut Vec<String>, workspace_id: &str) {
 
 async fn checkpoint_completed(pool: &PgPool, kind: &str, scope: &str) -> RuntimeResult<bool> {
   sqlx::query_scalar::<_, bool>(
-    "SELECT EXISTS(SELECT 1 FROM blob_reconciliation_checkpoints WHERE kind = $1 AND scope = $2 AND status = \
+    "SELECT EXISTS(SELECT 1 FROM storage_reconciliation_checkpoints WHERE kind = $1 AND scope = $2 AND status = \
      'completed')",
   )
   .bind(kind)
@@ -46,7 +46,43 @@ async fn checkpoint_completed(pool: &PgPool, kind: &str, scope: &str) -> Runtime
 }
 
 async fn projection_is_stale(pool: &PgPool, workspace_id: &str) -> RuntimeResult<bool> {
-  let checkpoint_fresh = checkpoint_completed(pool, "doc_blob_refs", workspace_id).await?;
+  let checkpoint_completed_at = sqlx::query_scalar::<_, Option<chrono::DateTime<chrono::Utc>>>(
+    r#"
+    SELECT MIN(completed_at)
+    FROM storage_reconciliation_checkpoints
+    WHERE scope = $1
+      AND kind IN ('document_cleanup', 'doc_blob_refs')
+      AND status = 'completed'
+    HAVING COUNT(*) = 2
+    "#,
+  )
+  .bind(workspace_id)
+  .fetch_optional(pool)
+  .await
+  .map_err(|err| RuntimeError::database("Blob cleanup retention checkpoint load failed", err))?
+  .flatten();
+  let Some(checkpoint_completed_at) = checkpoint_completed_at else {
+    return Ok(true);
+  };
+  let activity_after_checkpoint = sqlx::query_scalar::<_, bool>(
+    r#"
+    SELECT EXISTS(
+      SELECT 1 FROM snapshots
+      WHERE workspace_id = $1 AND updated_at > $2
+      UNION ALL
+      SELECT 1 FROM updates
+      WHERE workspace_id = $1 AND created_at > $2
+      UNION ALL
+      SELECT 1 FROM snapshot_histories
+      WHERE workspace_id = $1 AND timestamp > $2
+    )
+    "#,
+  )
+  .bind(workspace_id)
+  .bind(checkpoint_completed_at)
+  .fetch_one(pool)
+  .await
+  .map_err(|err| RuntimeError::database("Blob cleanup retention activity check failed", err))?;
   let has_stale_rows = sqlx::query_scalar::<_, bool>(
     "SELECT EXISTS(SELECT 1 FROM doc_blob_refs WHERE workspace_id = $1 AND status <> 'fresh')",
   )
@@ -54,7 +90,7 @@ async fn projection_is_stale(pool: &PgPool, workspace_id: &str) -> RuntimeResult
   .fetch_one(pool)
   .await
   .map_err(|err| RuntimeError::database("Blob cleanup projection freshness check failed", err))?;
-  Ok(!checkpoint_fresh || has_stale_rows)
+  Ok(activity_after_checkpoint || has_stale_rows)
 }
 
 async fn stale_projection_workspaces(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Vec<String>> {
@@ -170,7 +206,7 @@ async fn load_completed_blobs(
 
 async fn load_plan_cursor(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Option<String>> {
   let row = sqlx::query_as::<_, (String, serde_json::Value)>(
-    "SELECT status, cursor FROM blob_reconciliation_checkpoints WHERE kind = 'blob_cleanup_plan' AND scope = $1",
+    "SELECT status, cursor FROM storage_reconciliation_checkpoints WHERE kind = 'blob_cleanup_plan' AND scope = $1",
   )
   .bind(workspace_id)
   .fetch_optional(pool)
@@ -199,13 +235,13 @@ async fn upsert_plan_checkpoint(
   let status = if completed { "completed" } else { "running" };
   sqlx::query(
     r#"
-    INSERT INTO blob_reconciliation_checkpoints
+    INSERT INTO storage_reconciliation_checkpoints
       (kind, scope, status, cursor, last_key, completed_at)
     VALUES ('blob_cleanup_plan', $1, $2, $3, $4, CASE WHEN $5 THEN CURRENT_TIMESTAMP ELSE NULL END)
     ON CONFLICT (kind, scope) DO UPDATE
       SET status = EXCLUDED.status,
           cursor = EXCLUDED.cursor,
-          last_key = COALESCE(EXCLUDED.last_key, blob_reconciliation_checkpoints.last_key),
+          last_key = COALESCE(EXCLUDED.last_key, storage_reconciliation_checkpoints.last_key),
           completed_at = CASE WHEN $5 THEN CURRENT_TIMESTAMP ELSE NULL END,
           updated_at = CURRENT_TIMESTAMP
     "#,
@@ -224,7 +260,7 @@ async fn upsert_plan_checkpoint(
 async fn create_run(pool: &PgPool, workspace_id: &str) -> RuntimeResult<String> {
   sqlx::query_scalar::<_, String>(
     r#"
-    INSERT INTO blob_reconciliation_runs (kind, mode, status, workspace_id)
+    INSERT INTO storage_reconciliation_runs (kind, mode, status, workspace_id)
     VALUES ('blob_cleanup_plan', 'mark_only', 'running', $1)
     RETURNING id::text
     "#,
@@ -252,7 +288,7 @@ async fn finish_run(
   .unwrap_or(0);
   sqlx::query(
     r#"
-    UPDATE blob_reconciliation_runs
+    UPDATE storage_reconciliation_runs
     SET status = 'finished',
         finished_at = CURRENT_TIMESTAMP,
         scanned = $2,
@@ -318,7 +354,7 @@ async fn finish_execute_run(
 ) -> RuntimeResult<()> {
   sqlx::query(
     r#"
-    UPDATE blob_reconciliation_runs
+    UPDATE storage_reconciliation_runs
     SET status = 'finished',
         finished_at = CURRENT_TIMESTAMP,
         scanned = $2,

packages/backend/native/src/runtime/storage_runtime/blob_reconciliation.rs

@@ -85,7 +85,8 @@ impl BackfillCheckpoint {
 
 async fn load_checkpoint(pool: &PgPool, scope: &str) -> RuntimeResult<Option<BackfillCheckpoint>> {
   sqlx::query_as::<_, BackfillCheckpoint>(
-    "SELECT last_key, cursor FROM blob_reconciliation_checkpoints WHERE kind = 'blob_metadata_backfill' AND scope = $1",
+    "SELECT last_key, cursor FROM storage_reconciliation_checkpoints WHERE kind = 'blob_metadata_backfill' AND scope \
+     = $1",
   )
   .bind(scope)
   .fetch_optional(pool)
@@ -103,13 +104,13 @@ async fn upsert_checkpoint(
   let status = if completed { "completed" } else { "running" };
   sqlx::query(
     r#"
-    INSERT INTO blob_reconciliation_checkpoints
+    INSERT INTO storage_reconciliation_checkpoints
       (kind, scope, status, cursor, last_key, completed_at, metadata)
     VALUES ('blob_metadata_backfill', $1, $2, $3, $4, CASE WHEN $5 THEN CURRENT_TIMESTAMP ELSE NULL END, $6)
     ON CONFLICT (kind, scope) DO UPDATE
       SET status = EXCLUDED.status,
           cursor = EXCLUDED.cursor,
-          last_key = COALESCE(EXCLUDED.last_key, blob_reconciliation_checkpoints.last_key),
+          last_key = COALESCE(EXCLUDED.last_key, storage_reconciliation_checkpoints.last_key),
           completed_at = CASE WHEN $5 THEN CURRENT_TIMESTAMP ELSE NULL END,
           updated_at = CURRENT_TIMESTAMP,
           metadata = EXCLUDED.metadata
@@ -247,7 +248,7 @@ impl StorageRuntime {
 
     sqlx::query(
       r#"
-      INSERT INTO blob_reconciliation_runs
+      INSERT INTO storage_reconciliation_runs
         (kind, mode, status, workspace_id, finished_at, scanned, changed, failed, metadata)
       VALUES ('blob_metadata_backfill', 'execute', 'finished', $1, CURRENT_TIMESTAMP, $2, $3, $4, $5)
       "#,

packages/backend/native/src/runtime/storage_runtime/doc_blob_refs.rs

@@ -1,111 +1,32 @@
 use affine_doc_loader as doc_loader;
-use chrono::{DateTime, Utc};
+use sqlx::PgPool;
-use sqlx::{FromRow, PgPool};
-use y_octo::Doc;
 
-use super::{RuntimeDocBlobRefsResult, RuntimeError, RuntimeResult, StorageRuntime, napi_error};
+use super::{
+  CurrentDoc, RuntimeDocBlobRefsResult, RuntimeError, RuntimeResult, StorageRuntime, load_current_doc,
+  load_workspace_live_doc_ids, napi_error,
+};
 
 const PARSER_VERSION: i32 = 1;
 
-#[derive(FromRow)]
-struct SnapshotRow {
-  workspace_id: String,
-  doc_id: String,
-  blob: Vec<u8>,
-  updated_at: DateTime<Utc>,
-}
-
-#[derive(FromRow)]
-struct UpdateRow {
-  blob: Vec<u8>,
-  created_at: DateTime<Utc>,
-}
-
 struct ExtractedRef {
   blob_key: String,
   block_id: String,
   flavour: String,
 }
 
-async fn load_snapshot(pool: &PgPool, workspace_id: &str, doc_id: &str) -> RuntimeResult<Option<SnapshotRow>> {
+async fn load_workspace_doc_ids(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Vec<String>> {
-  sqlx::query_as::<_, SnapshotRow>(
+  let mut ids = load_workspace_live_doc_ids(pool, workspace_id).await?;
-    r#"
+  let retained = sqlx::query_scalar::<_, String>(
-    SELECT workspace_id, guid AS doc_id, blob, updated_at
+    "SELECT doc_id FROM document_cleanup_candidates WHERE workspace_id = $1 AND status IN ('marked', 'failed') ORDER \
-    FROM snapshots
+     BY doc_id",
-    WHERE workspace_id = $1 AND guid = $2
-    "#,
   )
   .bind(workspace_id)
-  .bind(doc_id)
-  .fetch_optional(pool)
-  .await
-  .map_err(|err| RuntimeError::database("Doc blob refs load snapshot failed", err))
-}
-
-async fn load_updates(pool: &PgPool, workspace_id: &str, doc_id: &str) -> RuntimeResult<Vec<UpdateRow>> {
-  sqlx::query_as::<_, UpdateRow>(
-    r#"
-    SELECT blob, created_at
-    FROM updates
-    WHERE workspace_id = $1 AND guid = $2
-    ORDER BY created_at ASC
-    "#,
-  )
-  .bind(workspace_id)
-  .bind(doc_id)
   .fetch_all(pool)
   .await
-  .map_err(|err| RuntimeError::database("Doc blob refs load updates failed", err))
+  .map_err(|err| RuntimeError::database("Doc blob refs candidate load failed", err))?;
-}
+  ids.extend(retained);
-
-fn apply_doc_updates(updates: impl IntoIterator<Item = Vec<u8>>) -> RuntimeResult<Vec<u8>> {
-  let mut doc = Doc::default();
-  for update in updates {
-    doc
-      .apply_update_from_binary_v1(&update)
-      .map_err(|err| RuntimeError::invalid_state(format!("Doc blob refs merge failed: {err}")))?;
-  }
-  doc
-    .encode_update_v1()
-    .map_err(|err| RuntimeError::invalid_state(format!("Doc blob refs encode failed: {err}")))
-}
-
-async fn load_current_doc(pool: &PgPool, workspace_id: &str, doc_id: &str) -> RuntimeResult<Option<SnapshotRow>> {
-  let snapshot = load_snapshot(pool, workspace_id, doc_id).await?;
-  let updates = load_updates(pool, workspace_id, doc_id).await?;
-  if snapshot.is_none() && updates.is_empty() {
-    return Ok(None);
-  }
-
-  let mut merge_inputs = Vec::with_capacity(updates.len() + usize::from(snapshot.is_some()));
-  let mut updated_at = snapshot
-    .as_ref()
-    .map(|snapshot| snapshot.updated_at)
-    .unwrap_or_else(Utc::now);
-  if let Some(snapshot) = snapshot {
-    merge_inputs.push(snapshot.blob);
-  }
-  for update in updates {
-    updated_at = update.created_at;
-    merge_inputs.push(update.blob);
-  }
-
-  Ok(Some(SnapshotRow {
-    workspace_id: workspace_id.to_string(),
-    doc_id: doc_id.to_string(),
-    blob: apply_doc_updates(merge_inputs)?,
-    updated_at,
-  }))
-}
-
-async fn load_workspace_doc_ids(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Vec<String>> {
-  let Some(root) = load_current_doc(pool, workspace_id, workspace_id).await? else {
-    return Ok(Vec::new());
-  };
-  let ids = doc_loader::get_doc_ids_from_binary(root.blob, true)
-    .map_err(|err| RuntimeError::invalid_state(format!("Doc blob refs root doc parse failed: {err}")))?;
-  let mut ids = ids;
   ids.sort();
+  ids.dedup();
   Ok(ids)
 }
 
@@ -124,7 +45,7 @@ async fn upsert_projection_checkpoint(
   };
   sqlx::query(
     r#"
-    INSERT INTO blob_reconciliation_checkpoints
+    INSERT INTO storage_reconciliation_checkpoints
       (kind, scope, status, cursor, completed_at, metadata)
     VALUES ('doc_blob_refs', $1, $2, $3, CASE WHEN $4 THEN CURRENT_TIMESTAMP ELSE NULL END, $5)
     ON CONFLICT (kind, scope) DO UPDATE
@@ -151,7 +72,7 @@ async fn upsert_projection_checkpoint(
 async fn upsert_projection_failure_checkpoint(pool: &PgPool, workspace_id: &str, error: &str) -> RuntimeResult<()> {
   sqlx::query(
     r#"
-    INSERT INTO blob_reconciliation_checkpoints
+    INSERT INTO storage_reconciliation_checkpoints
       (kind, scope, status, cursor, completed_at, metadata)
     VALUES ('doc_blob_refs', $1, 'failed', '{}', NULL, $2)
     ON CONFLICT (kind, scope) DO UPDATE
@@ -174,14 +95,17 @@ async fn upsert_projection_failure_checkpoint(pool: &PgPool, workspace_id: &str,
 }
 
 async fn load_projection_cursor(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Option<String>> {
-  let cursor = sqlx::query_scalar::<_, serde_json::Value>(
+  let checkpoint = sqlx::query_as::<_, (String, serde_json::Value)>(
-    "SELECT cursor FROM blob_reconciliation_checkpoints WHERE kind = 'doc_blob_refs' AND scope = $1",
+    "SELECT status, cursor FROM storage_reconciliation_checkpoints WHERE kind = 'doc_blob_refs' AND scope = $1",
   )
   .bind(workspace_id)
   .fetch_optional(pool)
   .await
   .map_err(|err| RuntimeError::database("Doc blob refs checkpoint load failed", err))?;
-  Ok(cursor.and_then(|cursor| {
+  Ok(checkpoint.and_then(|(status, cursor)| {
+    if status != "running" {
+      return None;
+    }
     cursor
       .get("lastDocId")
       .and_then(|value| value.as_str())
@@ -205,7 +129,7 @@ async fn purge_removed_doc_refs(pool: &PgPool, workspace_id: &str, current_doc_i
   Ok(result.rows_affected() as i64)
 }
 
-fn extract_refs(snapshot: &SnapshotRow) -> RuntimeResult<Vec<ExtractedRef>> {
+fn extract_refs(snapshot: &CurrentDoc) -> RuntimeResult<Vec<ExtractedRef>> {
   let parsed = doc_loader::parse_doc_from_binary(snapshot.blob.clone(), snapshot.doc_id.clone())
     .map_err(|err| RuntimeError::invalid_state(format!("Doc blob refs parse failed: {err}")))?;
   let mut refs = Vec::new();
@@ -226,6 +150,9 @@ fn extract_refs(snapshot: &SnapshotRow) -> RuntimeResult<Vec<ExtractedRef>> {
 
 #[cfg(test)]
 mod tests {
+  use chrono::Utc;
+  use y_octo::Doc;
+
   use super::*;
 
   #[test]
@@ -233,7 +160,7 @@ mod tests {
     let doc_id = "doc-blob-ref-test".to_string();
     let blob =
       doc_loader::build_full_doc("Doc", "![Alt](blob://image-blob-key)", &doc_id).expect("doc fixture should build");
-    let snapshot = SnapshotRow {
+    let snapshot = CurrentDoc {
       workspace_id: "workspace".to_string(),
       doc_id,
       blob,
@@ -272,9 +199,21 @@ mod tests {
     let ids = doc_loader::get_doc_ids_from_binary(root, true).expect("root doc ids should parse");
     assert_eq!(ids, vec!["active-doc", "trashed-doc"]);
   }
+
+  #[test]
+  fn doc_blob_refs_rejects_corrupt_docs() {
+    let snapshot = CurrentDoc {
+      workspace_id: "workspace".to_string(),
+      doc_id: "corrupt".to_string(),
+      blob: vec![0xff],
+      updated_at: Utc::now(),
+    };
+
+    assert!(extract_refs(&snapshot).is_err());
+  }
 }
 
-async fn replace_doc_refs(pool: &PgPool, snapshot: &SnapshotRow, refs: Vec<ExtractedRef>) -> RuntimeResult<(i64, i64)> {
+async fn replace_doc_refs(pool: &PgPool, snapshot: &CurrentDoc, refs: Vec<ExtractedRef>) -> RuntimeResult<(i64, i64)> {
   let mut tx = pool
     .begin()
     .await

packages/backend/native/src/runtime/storage_runtime/mod.rs

@@ -7,18 +7,21 @@ use std::{
 };
 
 use base64::{Engine as _, engine::general_purpose::URL_SAFE_NO_PAD};
+use chrono::{DateTime, Utc};
 use napi::bindgen_prelude::Buffer;
 use serde::Deserialize;
 use serde_json::{Map, Value};
 use sha2::{Digest, Sha256};
-use sqlx::{PgPool, Row, postgres::PgPoolOptions};
+use sqlx::{FromRow, PgPool, Row, postgres::PgPoolOptions};
 use tokio::{sync::Mutex, task::JoinSet};
+use y_octo::Doc;
 
 mod assetpack;
 mod blob_cleanup;
 mod blob_reclaimer;
 mod blob_reconciliation;
 mod doc_blob_refs;
+mod document_cleanup;
 pub(crate) mod object_storage;
 
 use self::object_storage::{
@@ -33,9 +36,10 @@ pub(super) use super::{
   napi_error, to_napi_error,
   types::{
     RuntimeBlobCleanupExecuteResult, RuntimeBlobCleanupPlanResult, RuntimeBlobCleanupResult, RuntimeBlobCompleteResult,
-    RuntimeBlobMetadataBackfillResult, RuntimeDocBlobRefsResult, RuntimeMultipartUploadInit,
+    RuntimeBlobMetadataBackfillResult, RuntimeDocBlobRefsResult, RuntimeDocumentCleanupAckResult,
-    RuntimeMultipartUploadPart, RuntimeObjectGetResult, RuntimeObjectListEntry, RuntimeObjectMetadata,
+    RuntimeDocumentCleanupEffect, RuntimeDocumentCleanupExecuteResult, RuntimeDocumentCleanupReconcileResult,
-    RuntimeObjectStoragePutOptions, RuntimePresignedObjectRequest,
+    RuntimeMultipartUploadInit, RuntimeMultipartUploadPart, RuntimeObjectGetResult, RuntimeObjectListEntry,
+    RuntimeObjectMetadata, RuntimeObjectStoragePutOptions, RuntimePresignedObjectRequest,
   },
 };
 
@@ -45,6 +49,100 @@ const OBJECT_DELETE_MANY_CONCURRENCY: usize = 3;
 
 type Result<T> = RuntimeResult<T>;
 
+#[derive(FromRow)]
+struct CurrentDoc {
+  workspace_id: String,
+  doc_id: String,
+  blob: Vec<u8>,
+  updated_at: DateTime<Utc>,
+}
+
+#[derive(FromRow)]
+struct CurrentDocUpdate {
+  blob: Vec<u8>,
+  created_at: DateTime<Utc>,
+}
+
+async fn load_current_doc(pool: &PgPool, workspace_id: &str, doc_id: &str) -> RuntimeResult<Option<CurrentDoc>> {
+  let snapshot = sqlx::query_as::<_, CurrentDoc>(
+    r#"
+    SELECT workspace_id, guid AS doc_id, blob, updated_at
+    FROM snapshots
+    WHERE workspace_id = $1 AND guid = $2
+    "#,
+  )
+  .bind(workspace_id)
+  .bind(doc_id)
+  .fetch_optional(pool)
+  .await
+  .map_err(|err| RuntimeError::database("Current doc snapshot load failed", err))?;
+  let updates = sqlx::query_as::<_, CurrentDocUpdate>(
+    r#"
+    SELECT blob, created_at
+    FROM updates
+    WHERE workspace_id = $1 AND guid = $2
+    ORDER BY created_at ASC
+    "#,
+  )
+  .bind(workspace_id)
+  .bind(doc_id)
+  .fetch_all(pool)
+  .await
+  .map_err(|err| RuntimeError::database("Current doc updates load failed", err))?;
+  merge_current_doc(workspace_id, doc_id, snapshot, updates)
+}
+
+fn merge_current_doc(
+  workspace_id: &str,
+  doc_id: &str,
+  snapshot: Option<CurrentDoc>,
+  updates: Vec<CurrentDocUpdate>,
+) -> RuntimeResult<Option<CurrentDoc>> {
+  if snapshot.is_none() && updates.is_empty() {
+    return Ok(None);
+  }
+  let mut doc = Doc::default();
+  let mut updated_at = snapshot
+    .as_ref()
+    .map(|snapshot| snapshot.updated_at)
+    .or_else(|| updates.first().map(|update| update.created_at))
+    .unwrap_or_else(Utc::now);
+  if let Some(snapshot) = &snapshot {
+    doc
+      .apply_update_from_binary_v1(&snapshot.blob)
+      .map_err(|err| RuntimeError::invalid_state(format!("Current doc snapshot merge failed: {err}")))?;
+  }
+  for update in updates {
+    updated_at = updated_at.max(update.created_at);
+    doc
+      .apply_update_from_binary_v1(&update.blob)
+      .map_err(|err| RuntimeError::invalid_state(format!("Current doc update merge failed: {err}")))?;
+  }
+  let blob = doc
+    .encode_update_v1()
+    .map_err(|err| RuntimeError::invalid_state(format!("Current doc encode failed: {err}")))?;
+
+  Ok(Some(CurrentDoc {
+    workspace_id: workspace_id.to_string(),
+    doc_id: doc_id.to_string(),
+    blob,
+    updated_at,
+  }))
+}
+
+async fn load_workspace_live_doc_ids(pool: &PgPool, workspace_id: &str) -> RuntimeResult<Vec<String>> {
+  workspace_live_doc_ids(load_current_doc(pool, workspace_id, workspace_id).await?)
+}
+
+fn workspace_live_doc_ids(root: Option<CurrentDoc>) -> RuntimeResult<Vec<String>> {
+  let root = root.ok_or_else(|| RuntimeError::invalid_state("Workspace root doc is missing"))?;
+  let mut ids = affine_doc_loader::get_doc_ids_from_binary(root.blob, true)
+    .map_err(|err| RuntimeError::invalid_state(format!("Workspace root doc parse failed: {err}")))?;
+  ids.sort();
+  ids.dedup();
+  Ok(ids)
+}
+
 #[napi_derive::napi(object)]
 pub struct StorageRuntimeHealth {
   pub started: bool,
@@ -1385,6 +1483,81 @@ fn system_time_ms(time: SystemTime) -> Result<i64> {
 mod tests {
   use super::*;
 
+  #[test]
+  fn workspace_live_set_merges_pending_updates_and_includes_trash() {
+    use y_octo::{Any, Value};
+
+    let snapshot = affine_doc_loader::add_doc_to_root_doc(Vec::new(), "live", None).unwrap();
+    let pending = affine_doc_loader::add_doc_to_root_doc(snapshot.clone(), "trash", None).unwrap();
+    let merged = merge_current_doc(
+      "workspace",
+      "workspace",
+      Some(CurrentDoc {
+        workspace_id: "workspace".to_string(),
+        doc_id: "workspace".to_string(),
+        blob: snapshot,
+        updated_at: Utc::now(),
+      }),
+      vec![CurrentDocUpdate {
+        blob: pending,
+        created_at: Utc::now(),
+      }],
+    )
+    .unwrap()
+    .unwrap();
+    let mut root = Doc::default();
+    root.apply_update_from_binary_v1(&merged.blob).unwrap();
+    let meta = root.get_map("meta").unwrap();
+    let mut pages = meta.get("pages").and_then(|value| value.to_array()).unwrap();
+    let mut trash = pages
+      .iter()
+      .find_map(|value| {
+        let page = value.to_map()?;
+        (page.get("id")?.to_any()? == Any::String("trash".to_string())).then_some(page)
+      })
+      .unwrap();
+    trash.insert("trash".to_string(), Value::Any(Any::True)).unwrap();
+
+    let ids = workspace_live_doc_ids(Some(CurrentDoc {
+      workspace_id: "workspace".to_string(),
+      doc_id: "workspace".to_string(),
+      blob: root.encode_update_v1().unwrap(),
+      updated_at: Utc::now(),
+    }))
+    .unwrap();
+    assert_eq!(ids, ["live", "trash"]);
+
+    let trash_index = pages
+      .iter()
+      .position(|value| {
+        value.to_map().and_then(|page| page.get("id")) == Some(Value::Any(Any::String("trash".to_string())))
+      })
+      .unwrap();
+    pages.remove(trash_index as u64, 1).unwrap();
+    let ids = workspace_live_doc_ids(Some(CurrentDoc {
+      workspace_id: "workspace".to_string(),
+      doc_id: "workspace".to_string(),
+      blob: root.encode_update_v1().unwrap(),
+      updated_at: Utc::now(),
+    }))
+    .unwrap();
+    assert_eq!(ids, ["live"]);
+  }
+
+  #[test]
+  fn workspace_live_set_fails_closed_for_missing_or_corrupt_root() {
+    assert!(workspace_live_doc_ids(None).is_err());
+    assert!(
+      workspace_live_doc_ids(Some(CurrentDoc {
+        workspace_id: "workspace".to_string(),
+        doc_id: "workspace".to_string(),
+        blob: vec![0xff],
+        updated_at: Utc::now(),
+      }))
+      .is_err()
+    );
+  }
+
   #[test]
   fn fs_key_normalization_rejects_traversal() {
     for (key, valid) in [

packages/backend/native/src/runtime/types.rs

@@ -243,6 +243,41 @@ pub struct RuntimeDocBlobRefsResult {
   pub next_cursor: Option<String>,
 }
 
+#[napi_derive::napi(object)]
+pub struct RuntimeDocumentCleanupReconcileResult {
+  pub scanned_docs: i64,
+  pub marked: i64,
+  pub reset: i64,
+  pub recovered: i64,
+}
+
+#[napi_derive::napi(object)]
+pub struct RuntimeDocumentCleanupEffect {
+  pub workspace_id: String,
+  pub doc_id: String,
+  pub cleanup_version: String,
+  pub comment_objects_done: bool,
+  pub search_done: bool,
+  pub copilot_done: bool,
+}
+
+#[napi_derive::napi(object)]
+pub struct RuntimeDocumentCleanupExecuteResult {
+  pub scanned_candidates: i64,
+  pub serialization_retries: i64,
+  pub executed: i64,
+  pub recovered: i64,
+  pub reset: i64,
+  pub failed: i64,
+  pub deleted_rows: i64,
+  pub effects: Vec<RuntimeDocumentCleanupEffect>,
+}
+
+#[napi_derive::napi(object)]
+pub struct RuntimeDocumentCleanupAckResult {
+  pub completed: bool,
+}
+
 #[napi_derive::napi(object)]
 pub struct RuntimeBlobCleanupPlanResult {
   pub run_id: Option<String>,

packages/backend/server/src/__tests__/copilot/copilot.spec.ts

@@ -28,7 +28,7 @@ import {
   WorkspaceModel,
   WorkspaceRole,
 } from '../../models';
-import type { LlmToolCallbackRequest } from '../../native';
+import { addDocToRootDoc, type LlmToolCallbackRequest } from '../../native';
 import { CopilotModule } from '../../plugins/copilot';
 import { CopilotContextService } from '../../plugins/copilot/context';
 import { CopilotContextResolver } from '../../plugins/copilot/context/resolver';
@@ -260,6 +260,80 @@ test.after.always(async t => {
   await t.context.module?.close();
 });
 
+test('document cleanup reconciles missing and restored copilot state before ack', async t => {
+  const { db, jobs, models, module, workspace } = t.context;
+  const queue = module.get(JobQueue);
+  const deleteEmbedding = Sinon.spy(
+    models.copilotContext,
+    'purgeWorkspaceEmbedding'
+  );
+  const scheduleEmbedding = Sinon.stub(
+    jobs,
+    'addDocEmbeddingQueueFromEvent'
+  ).resolves();
+
+  for (const [docId, restored, cleanupVersion] of [
+    ['missing-doc', false, 'missing-version'],
+    ['restored-doc', true, 'restored-version'],
+  ] as const) {
+    const ws = await workspace.create(userId);
+    const root = addDocToRootDoc(Buffer.from([0, 0]), docId, docId);
+    const missingRoot = addDocToRootDoc(
+      Buffer.from([0, 0]),
+      'live-doc',
+      'Live'
+    );
+    await db.snapshot.create({
+      data: {
+        workspaceId: ws.id,
+        id: ws.id,
+        blob: restored ? root : missingRoot,
+        state: Buffer.from([0, 0]),
+        updatedAt: new Date(),
+        createdAt: new Date(),
+      },
+    });
+    if (restored) {
+      await db.snapshot.create({
+        data: {
+          workspaceId: ws.id,
+          id: docId,
+          blob: addDocToRootDoc(Buffer.from([0, 0]), 'content', 'Content'),
+          state: Buffer.from([0, 0]),
+          updatedAt: new Date(),
+          createdAt: new Date(),
+        },
+      });
+    }
+
+    await jobs.reconcileDocumentCleanup({
+      workspaceId: ws.id,
+      docId,
+      cleanupVersion,
+    });
+
+    if (restored) {
+      t.true(scheduleEmbedding.calledOnceWith({ workspaceId: ws.id, docId }));
+      t.false(deleteEmbedding.called);
+    } else {
+      t.true(deleteEmbedding.calledOnceWith(ws.id, docId));
+      t.false(scheduleEmbedding.called);
+    }
+    const { payload } = await module.queue.waitFor(
+      'backendRuntime.ackDocumentCleanupEffect'
+    );
+    t.deepEqual(payload, {
+      workspaceId: ws.id,
+      docId,
+      cleanupVersion,
+      effect: 'copilot',
+    });
+    deleteEmbedding.resetHistory();
+    scheduleEmbedding.resetHistory();
+    (queue.add as Sinon.SinonStub).resetHistory();
+  }
+});
+
 test('MCP credentials stay bound to their endpoint, workspace, and profile', async t => {
   const { db, mcpCredentials, mcpProvider, models, workspace } = t.context;
   const ws = await workspace.create(userId);

packages/backend/server/src/__tests__/sync/gateway.spec.ts

@@ -671,7 +671,7 @@ test('active users metric should dedupe multiple sockets for one user', async t
 test('workspace sync delete-doc should enforce doc permissions', async t => {
   const db = app.get(PrismaClient);
   const models = app.get(Models);
-  const { user: owner } = await login(app);
+  const { user: owner, cookieHeader: ownerCookieHeader } = await login(app);
   const { user: collaborator, cookieHeader } = await login(app);
   const workspace = await models.workspace.create(owner.id);
   const docId = 'private-doc';
@@ -692,9 +692,10 @@ test('workspace sync delete-doc should enforce doc permissions', async t => {
   });
 
   const socket = createClient(url, cookieHeader);
+  const ownerSocket = createClient(url, ownerCookieHeader);
 
   try {
-    await waitForConnect(socket);
+    await Promise.all([waitForConnect(socket), waitForConnect(ownerSocket)]);
 
     const join = unwrapResponse(
       t,
@@ -719,8 +720,37 @@ test('workspace sync delete-doc should enforce doc permissions', async t => {
       })
     );
     t.true(error.message.includes('Doc.Delete'));
+
+    const ownerJoin = unwrapResponse(
+      t,
+      await emitWithAck<{ clientId: string; success: boolean }>(
+        ownerSocket,
+        'space:join',
+        {
+          spaceType: 'workspace',
+          spaceId: workspace.id,
+          clientVersion: '0.26.0',
+        }
+      )
+    );
+    t.true(ownerJoin.success);
+    unwrapResponse(
+      t,
+      await emitWithAck(ownerSocket, 'space:delete-doc', {
+        spaceType: 'workspace',
+        spaceId: workspace.id,
+        docId,
+      })
+    );
+    t.is(
+      await db.snapshot.count({
+        where: { workspaceId: workspace.id, id: docId },
+      }),
+      1
+    );
   } finally {
     socket.disconnect();
+    ownerSocket.disconnect();
   }
 });
 

packages/backend/server/src/core/doc/adapters/workspace.ts

@@ -137,8 +137,8 @@ export class PgWorkspaceDocStorageAdapter extends DocStorageAdapter {
     }));
   }
 
-  async deleteDoc(workspaceId: string, docId: string) {
+  async deleteDoc(_workspaceId: string, _docId: string) {
-    await this.models.doc.delete(workspaceId, docId);
+    return;
   }
 
   async deleteSpace(workspaceId: string) {

packages/backend/server/src/core/storage-runtime/provider.ts

@@ -258,6 +258,33 @@ export class StorageRuntimeProvider
     );
   }
 
+  async reconcileWorkspaceDocuments(workspaceId: string) {
+    return await this.measured('reconcileWorkspaceDocuments', rt =>
+      rt.reconcileWorkspaceDocuments(workspaceId)
+    );
+  }
+
+  async executeDocumentCleanupCandidates(
+    workspaceId: string | null | undefined,
+    gracePeriodDays: number,
+    limit: number
+  ) {
+    return await this.measured('executeDocumentCleanupCandidates', rt =>
+      rt.executeDocumentCleanupCandidates(workspaceId, gracePeriodDays, limit)
+    );
+  }
+
+  async ackDocumentCleanupEffect(
+    workspaceId: string,
+    docId: string,
+    cleanupVersion: string,
+    effect: 'search' | 'copilot'
+  ) {
+    return await this.measured('ackDocumentCleanupEffect', rt =>
+      rt.ackDocumentCleanupEffect(workspaceId, docId, cleanupVersion, effect)
+    );
+  }
+
   async planUnreferencedWorkspaceBlobs(
     workspaceId: string,
     gracePeriodDays: number,

packages/backend/server/src/core/storage/__tests__/blob-job.spec.ts

@@ -6,10 +6,13 @@ import { StorageBlobJob } from '../blob-job';
 interface Context {
   runtime: {
     health: Sinon.SinonStub;
+    reconcileWorkspaceDocuments: Sinon.SinonStub;
     backfillMissingBlobMetadata: Sinon.SinonStub;
     rebuildWorkspaceDocBlobRefs: Sinon.SinonStub;
     planUnreferencedWorkspaceBlobs: Sinon.SinonStub;
     executeBlobCleanupCandidates: Sinon.SinonStub;
+    executeDocumentCleanupCandidates: Sinon.SinonStub;
+    ackDocumentCleanupEffect: Sinon.SinonStub;
   };
   event: {
     emitAsync: Sinon.SinonStub;
@@ -35,10 +38,18 @@ test.beforeEach(t => {
       providerConfigured: true,
       provider: 'fs',
     }),
+    reconcileWorkspaceDocuments: Sinon.stub().resolves({
+      scannedDocs: 1,
+      marked: 0,
+      reset: 0,
+      recovered: 0,
+    }),
     backfillMissingBlobMetadata: Sinon.stub(),
     rebuildWorkspaceDocBlobRefs: Sinon.stub(),
     planUnreferencedWorkspaceBlobs: Sinon.stub(),
     executeBlobCleanupCandidates: Sinon.stub(),
+    executeDocumentCleanupCandidates: Sinon.stub(),
+    ackDocumentCleanupEffect: Sinon.stub(),
   };
   t.context.event = {
     emitAsync: Sinon.stub().resolves(undefined),
@@ -47,7 +58,18 @@ test.beforeEach(t => {
     add: Sinon.stub().resolves(undefined),
   };
   t.context.db = {
-    $queryRaw: Sinon.stub(),
+    $queryRaw: Sinon.stub().resolves([
+      {
+        marked: 0n,
+        failed: 0n,
+        effectsPending: 0n,
+        failedWorkspaceCheckpoints: 0n,
+        rootFailureCheckpoints: 0n,
+        staleProjectionBlocks: 0n,
+        oldestFailedSeconds: null,
+        oldestEffectsPendingSeconds: null,
+      },
+    ]),
     workspace: {
       findMany: Sinon.stub(),
     },
@@ -129,46 +151,6 @@ for (const scenario of objectStorageRequiredCases) {
   });
 }
 
-test('doc blob refs sweep continues after one workspace fails', async t => {
-  t.context.db.workspace.findMany.resolves([
-    { id: 'workspace-1', sid: 1 },
-    { id: 'workspace-2', sid: 2 },
-  ]);
-  t.context.runtime.rebuildWorkspaceDocBlobRefs
-    .onFirstCall()
-    .rejects(new Error('bad root doc'))
-    .onSecondCall()
-    .resolves({
-      scannedDocs: 1,
-      parsedDocs: 1,
-      refsWritten: 0,
-      refsDeleted: 0,
-      failedDocs: 0,
-      nextCursor: null,
-    });
-
-  await t.context.job.rebuildWorkspaceDocBlobRefsBySid({
-    workspaceLimit: 2,
-    docLimit: 100,
-  });
-
-  t.is(t.context.runtime.rebuildWorkspaceDocBlobRefs.callCount, 2);
-  t.deepEqual(t.context.runtime.rebuildWorkspaceDocBlobRefs.firstCall.args, [
-    'workspace-1',
-    100,
-  ]);
-  t.deepEqual(t.context.runtime.rebuildWorkspaceDocBlobRefs.secondCall.args, [
-    'workspace-2',
-    100,
-  ]);
-  t.true(
-    t.context.queue.add.calledWith(
-      'backendRuntime.rebuildWorkspaceDocBlobRefsBySid',
-      { lastSid: 2, workspaceLimit: 2, docLimit: 100 }
-    )
-  );
-});
-
 test('blob cleanup planning drains each workspace cursor before continuing', async t => {
   t.context.db.workspace.findMany.resolves([
     { id: 'workspace-1', sid: 1 },
@@ -229,6 +211,13 @@ test('blob cleanup planning drains each workspace cursor before continuing', asy
 test('daily blob cleanup execution uses a fixed job id', async t => {
   await t.context.job.dailyBlobCleanupExecution();
 
+  t.true(
+    t.context.queue.add.calledWith(
+      'backendRuntime.executeDocumentCleanupCandidates',
+      {},
+      { jobId: 'daily-backend-runtime-document-cleanup-execution' }
+    )
+  );
   t.true(
     t.context.queue.add.calledWith(
       'backendRuntime.executeBlobCleanupCandidatesByMarkedRuns',
@@ -238,6 +227,132 @@ test('daily blob cleanup execution uses a fixed job id', async t => {
   );
 });
 
+test('daily storage reconciliation uses a fixed job id', async t => {
+  await t.context.job.dailyStorageReconciliation();
+
+  t.true(
+    t.context.queue.add.calledWith(
+      'backendRuntime.reconcileWorkspaceStorageBySid',
+      {},
+      { jobId: 'daily-backend-runtime-storage-reconciliation' }
+    )
+  );
+});
+
+test('storage reconciliation orders document retention before blob cleanup', async t => {
+  t.context.db.workspace.findMany.resolves([{ id: 'workspace-1', sid: 1 }]);
+  t.context.runtime.rebuildWorkspaceDocBlobRefs.resolves({
+    scannedDocs: 1,
+    parsedDocs: 1,
+    refsWritten: 1,
+    refsDeleted: 0,
+    failedDocs: 0,
+    nextCursor: null,
+  });
+  t.context.runtime.planUnreferencedWorkspaceBlobs.resolves({
+    runId: 'run-1',
+    scannedBlobs: 1,
+    candidatesMarked: 0,
+    nextCursor: null,
+  });
+
+  await t.context.job.reconcileWorkspaceStorageBySid({ workspaceLimit: 10 });
+
+  Sinon.assert.callOrder(
+    t.context.runtime.reconcileWorkspaceDocuments,
+    t.context.runtime.rebuildWorkspaceDocBlobRefs,
+    t.context.runtime.planUnreferencedWorkspaceBlobs
+  );
+  t.pass();
+});
+
+test('storage reconciliation still refreshes document retention without object storage', async t => {
+  t.context.runtime.health.resolves({
+    databaseConnected: true,
+    providerConfigured: true,
+    provider: undefined,
+  });
+  t.context.db.workspace.findMany.resolves([{ id: 'workspace-1', sid: 1 }]);
+  t.context.runtime.rebuildWorkspaceDocBlobRefs.resolves({
+    scannedDocs: 1,
+    parsedDocs: 1,
+    refsWritten: 0,
+    refsDeleted: 0,
+    failedDocs: 0,
+    nextCursor: null,
+  });
+
+  await t.context.job.reconcileWorkspaceStorageBySid({});
+
+  t.true(t.context.runtime.reconcileWorkspaceDocuments.calledOnce);
+  t.true(t.context.runtime.rebuildWorkspaceDocBlobRefs.calledOnce);
+  t.false(t.context.runtime.planUnreferencedWorkspaceBlobs.called);
+});
+
+test('document cleanup dispatches independent stable search and copilot effects', async t => {
+  t.context.runtime.executeDocumentCleanupCandidates.resolves({
+    scannedCandidates: 1,
+    serializationRetries: 0,
+    executed: 1,
+    recovered: 0,
+    reset: 0,
+    failed: 0,
+    deletedRows: 3,
+    effects: [
+      {
+        workspaceId: 'workspace-1',
+        docId: 'doc-1',
+        cleanupVersion: 'version-1',
+        commentObjectsDone: true,
+        searchDone: false,
+        copilotDone: false,
+      },
+    ],
+  });
+
+  await t.context.job.executeDocumentCleanupCandidates({});
+
+  t.true(
+    t.context.queue.add.calledWith(
+      'indexer.reconcileDocumentCleanup',
+      Sinon.match({ docId: 'doc-1' }),
+      {
+        jobId: 'document-cleanup:search:workspace-1:doc-1:version-1',
+      }
+    )
+  );
+  t.true(
+    t.context.queue.add.calledWith(
+      'copilot.embedding.reconcileDocumentCleanup',
+      Sinon.match({ docId: 'doc-1' }),
+      {
+        jobId: 'document-cleanup:copilot:workspace-1:doc-1:version-1',
+      }
+    )
+  );
+  t.true(
+    t.context.event.emitAsync.calledWith('workspace.blobs.updated', {
+      workspaceId: 'workspace-1',
+    })
+  );
+});
+
+test('document cleanup effect ack delegates to storage runtime', async t => {
+  await t.context.job.ackDocumentCleanupEffect({
+    workspaceId: 'workspace-1',
+    docId: 'doc-1',
+    cleanupVersion: 'version-1',
+    effect: 'search',
+  });
+
+  t.deepEqual(t.context.runtime.ackDocumentCleanupEffect.firstCall.args, [
+    'workspace-1',
+    'doc-1',
+    'version-1',
+    'search',
+  ]);
+});
+
 test('blob cleanup execution sweep drains marked runs and continues by page', async t => {
   t.context.db.$queryRaw
     .onFirstCall()

packages/backend/server/src/core/storage/blob-job.ts

@@ -2,7 +2,7 @@ import { Injectable, Logger } from '@nestjs/common';
 import { Cron, CronExpression } from '@nestjs/schedule';
 import { PrismaClient } from '@prisma/client';
 
-import { EventBus, JobQueue, OnJob } from '../../base';
+import { EventBus, JobQueue, metrics, OnJob } from '../../base';
 import { StorageRuntimeProvider } from '../storage-runtime';
 
 // Queue keys are persisted API; keep the legacy backendRuntime.* names while
@@ -18,15 +18,22 @@ declare global {
       workspaceLimit?: number;
       objectLimit?: number;
     };
-    'backendRuntime.rebuildWorkspaceDocBlobRefs': {
+    'backendRuntime.reconcileWorkspaceStorageBySid': {
-      workspaceId: string;
-      limit?: number;
-    };
-    'backendRuntime.rebuildWorkspaceDocBlobRefsBySid': {
       lastSid?: number;
       workspaceLimit?: number;
       docLimit?: number;
     };
+    'backendRuntime.executeDocumentCleanupCandidates': {
+      workspaceId?: string;
+      gracePeriodDays?: number;
+      limit?: number;
+    };
+    'backendRuntime.ackDocumentCleanupEffect': {
+      workspaceId: string;
+      docId: string;
+      cleanupVersion: string;
+      effect: 'search' | 'copilot';
+    };
     'backendRuntime.planUnreferencedWorkspaceBlobs': {
       workspaceId: string;
       gracePeriodDays?: number;
@@ -89,25 +96,6 @@ export class StorageBlobJob {
     });
   }
 
-  async enqueueRebuildWorkspaceDocBlobRefs(workspaceId: string, limit = 1000) {
-    await this.queue.add('backendRuntime.rebuildWorkspaceDocBlobRefs', {
-      workspaceId,
-      limit,
-    });
-  }
-
-  async enqueueRebuildWorkspaceDocBlobRefsBySid(
-    lastSid = 0,
-    workspaceLimit = 100,
-    docLimit = 1000
-  ) {
-    await this.queue.add('backendRuntime.rebuildWorkspaceDocBlobRefsBySid', {
-      lastSid,
-      workspaceLimit,
-      docLimit,
-    });
-  }
-
   @OnJob('backendRuntime.backfillMissingBlobMetadataBySid')
   async backfillMissingBlobMetadataBySid({
     lastSid = 0,
@@ -211,25 +199,21 @@ export class StorageBlobJob {
   }
 
   @Cron(CronExpression.EVERY_DAY_AT_2AM)
-  async dailyDocBlobRefsRebuild() {
+  async dailyStorageReconciliation() {
     await this.queue.add(
-      'backendRuntime.rebuildWorkspaceDocBlobRefsBySid',
+      'backendRuntime.reconcileWorkspaceStorageBySid',
       {},
-      { jobId: 'daily-backend-runtime-doc-blob-refs-rebuild' }
+      { jobId: 'daily-backend-runtime-storage-reconciliation' }
-    );
-  }
-
-  @Cron(CronExpression.EVERY_DAY_AT_3AM)
-  async dailyBlobCleanupPlanning() {
-    await this.queue.add(
-      'backendRuntime.planUnreferencedWorkspaceBlobsBySid',
-      {},
-      { jobId: 'daily-backend-runtime-blob-cleanup-planning' }
     );
   }
 
   @Cron(CronExpression.EVERY_DAY_AT_4AM)
   async dailyBlobCleanupExecution() {
+    await this.queue.add(
+      'backendRuntime.executeDocumentCleanupCandidates',
+      {},
+      { jobId: 'daily-backend-runtime-document-cleanup-execution' }
+    );
     await this.queue.add(
       'backendRuntime.executeBlobCleanupCandidatesByMarkedRuns',
       {},
@@ -249,44 +233,39 @@ export class StorageBlobJob {
     await this.drainBlobMetadataBackfill(workspaceId, limit);
   }
 
-  @OnJob('backendRuntime.rebuildWorkspaceDocBlobRefs')
+  @OnJob('backendRuntime.reconcileWorkspaceStorageBySid')
-  async rebuildWorkspaceDocBlobRefs({
+  async reconcileWorkspaceStorageBySid({
-    workspaceId,
-    limit = 1000,
-  }: Jobs['backendRuntime.rebuildWorkspaceDocBlobRefs']) {
-    await this.drainWorkspaceDocBlobRefs(workspaceId, limit);
-  }
-
-  @OnJob('backendRuntime.rebuildWorkspaceDocBlobRefsBySid')
-  async rebuildWorkspaceDocBlobRefsBySid({
     lastSid = 0,
     workspaceLimit = 100,
     docLimit = 1000,
-  }: Jobs['backendRuntime.rebuildWorkspaceDocBlobRefsBySid']) {
+  }: Jobs['backendRuntime.reconcileWorkspaceStorageBySid']) {
     const workspaces = await this.db.workspace.findMany({
-      where: {
+      where: { sid: { gt: lastSid } },
-        sid: {
+      orderBy: { sid: 'asc' },
-          gt: lastSid,
+      select: { id: true, sid: true },
-        },
-      },
-      orderBy: {
-        sid: 'asc',
-      },
-      select: {
-        id: true,
-        sid: true,
-      },
       take: workspaceLimit,
     });
+    const objectStorageConfigured = await this.hasObjectStorage(
+      'storage reconciliation blob cleanup planning'
+    );
 
     for (const workspace of workspaces) {
       try {
+        await this.rt.reconcileWorkspaceDocuments(workspace.id);
         await this.drainWorkspaceDocBlobRefs(workspace.id, docLimit, {
           sid: workspace.sid,
         });
+        if (objectStorageConfigured) {
+          await this.drainBlobCleanupPlanning(workspace.id, 30, 1000, {
+            sid: workspace.sid,
+          });
+        }
       } catch (err) {
+        metrics.storage
+          .counter('document_cleanup_workspace_failure_total')
+          .add(1);
         this.logger.error(
-          `doc blob refs rebuild failed workspace=${workspace.id} sid=${workspace.sid}`,
+          `storage reconciliation failed workspace=${workspace.id} sid=${workspace.sid}`,
           err
         );
       }
@@ -294,14 +273,71 @@ export class StorageBlobJob {
 
     const nextSid = workspaces.at(-1)?.sid;
     if (nextSid !== undefined && workspaces.length === workspaceLimit) {
-      await this.enqueueRebuildWorkspaceDocBlobRefsBySid(
+      await this.queue.add('backendRuntime.reconcileWorkspaceStorageBySid', {
-        nextSid,
+        lastSid: nextSid,
         workspaceLimit,
-        docLimit
+        docLimit,
-      );
+      });
     }
   }
 
+  @OnJob('backendRuntime.executeDocumentCleanupCandidates')
+  async executeDocumentCleanupCandidates({
+    workspaceId,
+    gracePeriodDays = 30,
+    limit = 100,
+  }: Jobs['backendRuntime.executeDocumentCleanupCandidates']) {
+    const result = await this.rt.executeDocumentCleanupCandidates(
+      workspaceId,
+      gracePeriodDays,
+      limit
+    );
+    metrics.storage
+      .counter('document_cleanup_serialization_retry_total')
+      .add(result.serializationRetries);
+    metrics.storage
+      .counter('document_cleanup_execute_failure_total')
+      .add(result.failed);
+    for (const effect of result.effects) {
+      if (!effect.searchDone) {
+        await this.queue.add('indexer.reconcileDocumentCleanup', effect, {
+          jobId: `document-cleanup:search:${effect.workspaceId}:${effect.docId}:${effect.cleanupVersion}`,
+        });
+      }
+      if (!effect.copilotDone) {
+        await this.queue.add(
+          'copilot.embedding.reconcileDocumentCleanup',
+          effect,
+          {
+            jobId: `document-cleanup:copilot:${effect.workspaceId}:${effect.docId}:${effect.cleanupVersion}`,
+          }
+        );
+      }
+      if (effect.commentObjectsDone) {
+        await this.event.emitAsync('workspace.blobs.updated', {
+          workspaceId: effect.workspaceId,
+        });
+      }
+    }
+    await this.recordDocumentCleanupHealth();
+    return result;
+  }
+
+  @OnJob('backendRuntime.ackDocumentCleanupEffect')
+  async ackDocumentCleanupEffect({
+    workspaceId,
+    docId,
+    cleanupVersion,
+    effect,
+  }: Jobs['backendRuntime.ackDocumentCleanupEffect']) {
+    await this.rt.ackDocumentCleanupEffect(
+      workspaceId,
+      docId,
+      cleanupVersion,
+      effect
+    );
+  }
+
   @OnJob('backendRuntime.planUnreferencedWorkspaceBlobs')
   async planUnreferencedWorkspaceBlobs({
     workspaceId,
@@ -545,6 +581,82 @@ export class StorageBlobJob {
     return rows.map(row => row.runId);
   }
 
+  private async recordDocumentCleanupHealth() {
+    const [health] = await this.db.$queryRaw<
+      {
+        marked: bigint;
+        failed: bigint;
+        effectsPending: bigint;
+        failedWorkspaceCheckpoints: bigint;
+        rootFailureCheckpoints: bigint;
+        staleProjectionBlocks: bigint;
+        oldestFailedSeconds: number | null;
+        oldestEffectsPendingSeconds: number | null;
+      }[]
+    >`
+      SELECT
+        COUNT(*) FILTER (WHERE status = 'marked') AS marked,
+        COUNT(*) FILTER (WHERE status = 'failed') AS failed,
+        COUNT(*) FILTER (WHERE status = 'effects_pending') AS "effectsPending",
+        EXTRACT(EPOCH FROM CURRENT_TIMESTAMP -
+          MIN(updated_at) FILTER (WHERE status = 'failed'))::double precision AS "oldestFailedSeconds",
+        EXTRACT(EPOCH FROM CURRENT_TIMESTAMP -
+          MIN(updated_at) FILTER (WHERE status = 'effects_pending'))::double precision AS "oldestEffectsPendingSeconds",
+        (SELECT COUNT(*) FROM storage_reconciliation_checkpoints
+          WHERE kind = 'document_cleanup' AND status = 'failed') AS "failedWorkspaceCheckpoints",
+        (SELECT COUNT(*) FROM storage_reconciliation_checkpoints
+          WHERE kind = 'document_cleanup' AND status = 'failed'
+            AND metadata->>'failureKind' = 'root') AS "rootFailureCheckpoints",
+        (SELECT COUNT(*) FROM storage_reconciliation_runs
+          WHERE kind = 'blob_cleanup_plan'
+            AND started_at >= CURRENT_TIMESTAMP - INTERVAL '1 day'
+            AND jsonb_array_length(COALESCE(metadata->'staleOrFailedProjectionWorkspaces', '[]')) > 0
+        ) AS "staleProjectionBlocks"
+      FROM document_cleanup_candidates
+    `;
+    if (!health) {
+      return;
+    }
+    for (const [name, value] of [
+      ['document_cleanup_marked', health.marked],
+      ['document_cleanup_failed', health.failed],
+      ['document_cleanup_effects_pending', health.effectsPending],
+      [
+        'document_cleanup_failed_workspace_checkpoints',
+        health.failedWorkspaceCheckpoints,
+      ],
+      [
+        'document_cleanup_root_failure_checkpoints',
+        health.rootFailureCheckpoints,
+      ],
+      [
+        'document_cleanup_stale_projection_blocks',
+        health.staleProjectionBlocks,
+      ],
+    ] as const) {
+      metrics.storage.gauge(name).record(Number(value));
+    }
+    metrics.storage
+      .gauge('document_cleanup_oldest_failed_seconds')
+      .record(health.oldestFailedSeconds ?? 0);
+    metrics.storage
+      .gauge('document_cleanup_oldest_effects_pending_seconds')
+      .record(health.oldestEffectsPendingSeconds ?? 0);
+
+    if (
+      health.failedWorkspaceCheckpoints > 0n ||
+      health.rootFailureCheckpoints > 0n ||
+      health.staleProjectionBlocks > 0n ||
+      (health.oldestFailedSeconds ?? 0) >= 86_400 ||
+      (health.oldestEffectsPendingSeconds ?? 0) >= 86_400 ||
+      health.marked >= 10_000n
+    ) {
+      this.logger.warn(
+        `document cleanup health marked=${health.marked} failed=${health.failed} effectsPending=${health.effectsPending} failedWorkspaceCheckpoints=${health.failedWorkspaceCheckpoints} rootFailureCheckpoints=${health.rootFailureCheckpoints} staleProjectionBlocks=${health.staleProjectionBlocks} oldestFailedSeconds=${health.oldestFailedSeconds ?? 0} oldestEffectsPendingSeconds=${health.oldestEffectsPendingSeconds ?? 0}`
+      );
+    }
+  }
+
   private async hasMarkedBlobCleanupCandidates() {
     const rows = await this.db.$queryRaw<{ exists: boolean }[]>`
       SELECT EXISTS(

packages/backend/server/src/core/utils/__tests__/blocksute.spec.ts

@@ -1,5 +1,6 @@
 import test from 'ava';
 import { omit } from 'lodash-es';
+import * as Y from 'yjs';
 
 import { createModule } from '../../../__tests__/create-module';
 import { Mockers } from '../../../__tests__/mocks';
@@ -38,6 +39,86 @@ test('can read all doc ids from workspace snapshot', async t => {
   t.snapshot(docIds);
 });
 
+test('merged root updates retain trash and exclude permanently removed docs', async t => {
+  const rootDoc = await models.doc.get(workspace.id, workspace.id);
+  t.truthy(rootDoc);
+
+  const root = new Y.Doc();
+  Y.applyUpdate(root, rootDoc!.blob);
+  const pending = new Y.Doc();
+  Y.applyUpdate(pending, Y.encodeStateAsUpdate(root));
+  const trashMeta = new Y.Map<unknown>();
+  trashMeta.set('id', 'trash-doc');
+  trashMeta.set('title', 'Trash');
+  trashMeta.set('trash', true);
+  (pending.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>).push([
+    trashMeta,
+  ]);
+  const pendingUpdate = Y.encodeStateAsUpdate(
+    pending,
+    Y.encodeStateVector(root)
+  );
+  const merged = Y.mergeUpdates([rootDoc!.blob, pendingUpdate]);
+
+  t.false(readAllDocIdsFromWorkspaceSnapshot(merged).includes('trash-doc'));
+  t.true(
+    readAllDocIdsFromWorkspaceSnapshot(merged, true).includes('trash-doc')
+  );
+
+  const removed = new Y.Doc();
+  Y.applyUpdate(removed, merged);
+  const pages = removed.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>;
+  const target = pages
+    .toArray()
+    .findIndex(meta => meta instanceof Y.Map && meta.get('id') === 'trash-doc');
+  pages.delete(target, 1);
+  t.false(
+    readAllDocIdsFromWorkspaceSnapshot(
+      Y.encodeStateAsUpdate(removed),
+      true
+    ).includes('trash-doc')
+  );
+});
+
+test('nested concurrent meta edits do not restore a deleted entry', t => {
+  const initial = new Y.Doc();
+  const pages = new Y.Array<Y.Map<unknown>>();
+  const meta = new Y.Map<unknown>();
+  meta.set('id', 'doc-1');
+  meta.set('title', 'Initial');
+  pages.push([meta]);
+  initial.getMap('meta').set('pages', pages);
+  const state = Y.encodeStateAsUpdate(initial);
+
+  const deletingClient = new Y.Doc();
+  const editingClient = new Y.Doc();
+  Y.applyUpdate(deletingClient, state);
+  Y.applyUpdate(editingClient, state);
+  (
+    deletingClient.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>
+  ).delete(0, 1);
+  (editingClient.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>)
+    .get(0)
+    .set('title', 'Offline edit');
+
+  const merged = new Y.Doc();
+  Y.applyUpdate(merged, Y.encodeStateAsUpdate(deletingClient));
+  Y.applyUpdate(merged, Y.encodeStateAsUpdate(editingClient));
+  t.is(
+    (merged.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>).length,
+    0
+  );
+
+  (editingClient.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>).push([
+    meta.clone(),
+  ]);
+  Y.applyUpdate(merged, Y.encodeStateAsUpdate(editingClient));
+  t.is(
+    (merged.getMap('meta').get('pages') as Y.Array<Y.Map<unknown>>).length,
+    1
+  );
+});
+
 test('can read all blocks from doc snapshot', async t => {
   const rootDoc = await models.doc.get(workspace.id, workspace.id);
   t.truthy(rootDoc);

packages/backend/server/src/core/utils/blocksuite.ts

@@ -45,8 +45,11 @@ export function parsePageDoc(
   );
 }
 
-export function readAllDocIdsFromWorkspaceSnapshot(snapshot: Uint8Array) {
+export function readAllDocIdsFromWorkspaceSnapshot(
-  return readAllDocIdsFromRootDoc(Buffer.from(snapshot), false);
+  snapshot: Uint8Array,
+  includeTrash = false
+) {
+  return readAllDocIdsFromRootDoc(Buffer.from(snapshot), includeTrash);
 }
 
 function safeParseJson<T>(str: string): T | undefined {

packages/backend/server/src/models/copilot-context.ts

@@ -337,10 +337,14 @@ export class CopilotContextModel extends BaseModel {
   }
 
   async deleteWorkspaceEmbedding(workspaceId: string, docId: string) {
+    await this.purgeWorkspaceEmbedding(workspaceId, docId);
+    await this.fulfillEmptyEmbedding(workspaceId, docId);
+  }
+
+  async purgeWorkspaceEmbedding(workspaceId: string, docId: string) {
     await this.db.aiWorkspaceEmbedding.deleteMany({
       where: { workspaceId, docId },
     });
-    await this.fulfillEmptyEmbedding(workspaceId, docId);
   }
 
   async matchWorkspaceEmbedding(

packages/backend/server/src/plugins/copilot/embedding/job.ts

@@ -205,20 +205,49 @@ export class CopilotEmbeddingJob {
     );
   }
 
-  @OnJob('copilot.embedding.deleteDoc')
+  private async deleteDocEmbedding(doc: {
-  async deleteDocEmbeddingQueueFromEvent(
+    workspaceId: string;
-    doc: Jobs['copilot.embedding.deleteDoc']
+    docId: string;
-  ) {
+  }) {
     await this.queue.remove(
       `workspace:embedding:${doc.workspaceId}:${doc.docId}`,
       'copilot.embedding.docs'
     );
-    await this.models.copilotContext.deleteWorkspaceEmbedding(
+    await this.models.copilotContext.purgeWorkspaceEmbedding(
       doc.workspaceId,
       doc.docId
     );
   }
 
+  @OnJob('copilot.embedding.reconcileDocumentCleanup')
+  async reconcileDocumentCleanup({
+    workspaceId,
+    docId,
+    cleanupVersion,
+  }: Jobs['copilot.embedding.reconcileDocumentCleanup']) {
+    const root = await this.doc.getDoc(workspaceId, workspaceId);
+    if (!root) {
+      throw new Error(`workspace root ${workspaceId} not found`);
+    }
+    const live = readAllDocIdsFromWorkspaceSnapshot(root.bin, true).includes(
+      docId
+    );
+    if (live) {
+      if (!(await this.doc.getDoc(workspaceId, docId))) {
+        throw new Error(`restored document ${workspaceId}/${docId} not found`);
+      }
+      await this.addDocEmbeddingQueueFromEvent({ workspaceId, docId });
+    } else {
+      await this.deleteDocEmbedding({ workspaceId, docId });
+    }
+    await this.queue.add('backendRuntime.ackDocumentCleanupEffect', {
+      workspaceId,
+      docId,
+      cleanupVersion,
+      effect: 'copilot',
+    });
+  }
+
   private async readCopilotBlob(
     userId: string,
     workspaceId: string,

packages/backend/server/src/plugins/copilot/embedding/types.ts

@@ -68,9 +68,10 @@ declare global {
       docId: string;
     };
 
-    'copilot.embedding.deleteDoc': {
+    'copilot.embedding.reconcileDocumentCleanup': {
       workspaceId: string;
       docId: string;
+      cleanupVersion: string;
     };
 
     'copilot.embedding.files': {

packages/backend/server/src/plugins/copilot/session.ts

@@ -39,10 +39,6 @@ declare global {
     'copilot.session.generateTitle': {
       sessionId: string;
     };
-    'copilot.session.deleteDoc': {
-      workspaceId: string;
-      docId: string;
-    };
   }
 }
 
@@ -512,23 +508,6 @@ export class ChatSessionService {
     return null;
   }
 
-  @OnJob('copilot.session.deleteDoc')
-  async deleteDocSessions(doc: Jobs['copilot.session.deleteDoc']) {
-    const sessionIds = await this.models.copilotSession
-      .list({
-        userId: undefined,
-        workspaceId: doc.workspaceId,
-        docId: doc.docId,
-      })
-      .then(s => s.map(s => [s.userId, s.id]));
-    for (const [userId, sessionId] of sessionIds) {
-      await this.models.copilotSession.update(
-        { userId, sessionId, docId: null },
-        true
-      );
-    }
-  }
-
   @OnJob('copilot.session.generateTitle')
   async generateSessionTitle(job: Jobs['copilot.session.generateTitle']) {
     const { sessionId } = job;

packages/backend/server/src/plugins/indexer/__tests__/job.spec.ts

@@ -6,14 +6,17 @@ import Sinon from 'sinon';
 
 import { createModule } from '../../../__tests__/create-module';
 import { Mockers } from '../../../__tests__/mocks';
-import { JOB_SIGNAL } from '../../../base';
+import { Config, JOB_SIGNAL } from '../../../base';
 import { ConfigModule } from '../../../base/config';
 import { ServerConfigModule } from '../../../core/config';
+import { DocReader } from '../../../core/doc';
 import { Models } from '../../../models';
+import { addDocToRootDoc } from '../../../native';
 import { SearchProviderFactory } from '../factory';
 import { IndexerModule, IndexerService } from '../index';
 import { IndexerJob } from '../job';
 import { ManticoresearchProvider } from '../providers';
+import { blockSQL, docSQL, SearchTable } from '../tables';
 
 const module = await createModule({
   imports: [
@@ -32,6 +35,8 @@ const indexerJob = module.get(IndexerJob);
 const searchProviderFactory = module.get(SearchProviderFactory);
 const manticoresearch = module.get(ManticoresearchProvider);
 const models = module.get(Models);
+const docReader = module.get(DocReader);
+const config = module.get(Config);
 
 const user = await module.create(Mockers.User);
 const workspace = await module.create(Mockers.Workspace, {
@@ -39,6 +44,11 @@ const workspace = await module.create(Mockers.Workspace, {
   owner: user,
 });
 
+test.before(async () => {
+  await manticoresearch.recreateTable(SearchTable.block, blockSQL);
+  await manticoresearch.recreateTable(SearchTable.doc, docSQL);
+});
+
 test.after.always(async () => {
   await module.close();
 });
@@ -105,7 +115,7 @@ test('should not sync existing doc', async t => {
   t.is(module.queue.count('indexer.indexDoc'), count);
 });
 
-test('should delete doc from indexer when docId is not in workspace', async t => {
+test('should delete dangling indexed docs absent from the root live set', async t => {
   const count = module.queue.count('indexer.deleteDoc');
   mock.method(indexerService, 'listDocIds', async () => {
     return ['mock-doc-id1', 'mock-doc-id2'];
@@ -121,6 +131,104 @@ test('should delete doc from indexer when docId is not in workspace', async t =>
   t.is(module.queue.count('indexer.deleteDoc'), count + 2);
 });
 
+test('document cleanup reconcile deletes missing search state before ack', async t => {
+  const deleteSpy = Sinon.spy(indexerService, 'deleteDoc');
+  const indexSpy = Sinon.spy(indexerService, 'indexDoc');
+  const cleanupWorkspace = await module.create(Mockers.Workspace, {
+    owner: user,
+  });
+  await module.create(Mockers.DocSnapshot, {
+    workspaceId: cleanupWorkspace.id,
+    docId: cleanupWorkspace.id,
+    user,
+    blob: addDocToRootDoc(Buffer.from([0, 0]), 'live-doc', 'Live'),
+  });
+
+  await indexerJob.reconcileDocumentCleanup({
+    workspaceId: cleanupWorkspace.id,
+    docId: 'missing-doc',
+    cleanupVersion: 'version-1',
+  });
+
+  t.true(deleteSpy.calledOnceWith(cleanupWorkspace.id, 'missing-doc'));
+  t.false(indexSpy.called);
+  const { payload } = await module.queue.waitFor(
+    'backendRuntime.ackDocumentCleanupEffect'
+  );
+  t.deepEqual(payload, {
+    workspaceId: cleanupWorkspace.id,
+    docId: 'missing-doc',
+    cleanupVersion: 'version-1',
+    effect: 'search',
+  });
+});
+
+test('document cleanup reconcile reindexes restored doc before ack', async t => {
+  const deleteSpy = Sinon.spy(indexerService, 'deleteDoc');
+  const indexSpy = Sinon.spy(indexerService, 'indexDoc');
+  const cleanupWorkspace = await module.create(Mockers.Workspace, {
+    owner: user,
+  });
+  await module.create(Mockers.DocSnapshot, {
+    workspaceId: cleanupWorkspace.id,
+    docId: cleanupWorkspace.id,
+    user,
+    blob: addDocToRootDoc(Buffer.from([0, 0]), 'restored-doc', 'Restored'),
+  });
+  await module.create(Mockers.DocSnapshot, {
+    workspaceId: cleanupWorkspace.id,
+    docId: 'restored-doc',
+    user,
+  });
+  const getDocSpy = Sinon.spy(docReader, 'getDoc');
+
+  await indexerJob.reconcileDocumentCleanup({
+    workspaceId: cleanupWorkspace.id,
+    docId: 'restored-doc',
+    cleanupVersion: 'version-2',
+  });
+
+  t.true(indexSpy.calledOnceWith(cleanupWorkspace.id, 'restored-doc'));
+  t.false(deleteSpy.called);
+  t.true(getDocSpy.calledWith(cleanupWorkspace.id, cleanupWorkspace.id));
+  t.true(getDocSpy.calledWith(cleanupWorkspace.id, 'restored-doc'));
+  const { payload } = await module.queue.waitFor(
+    'backendRuntime.ackDocumentCleanupEffect'
+  );
+  t.deepEqual(payload, {
+    workspaceId: cleanupWorkspace.id,
+    docId: 'restored-doc',
+    cleanupVersion: 'version-2',
+    effect: 'search',
+  });
+});
+
+test('document cleanup reconcile only acknowledges when indexer is disabled', async t => {
+  Sinon.stub(config.indexer, 'enabled').value(false);
+  const deleteSpy = Sinon.spy(indexerService, 'deleteDoc');
+  const indexSpy = Sinon.spy(indexerService, 'indexDoc');
+  const getDocSpy = Sinon.spy(docReader, 'getDoc');
+
+  await indexerJob.reconcileDocumentCleanup({
+    workspaceId: workspace.id,
+    docId: 'disabled-doc',
+    cleanupVersion: 'version-disabled',
+  });
+
+  t.false(deleteSpy.called);
+  t.false(indexSpy.called);
+  t.false(getDocSpy.called);
+  const { payload } = await module.queue.waitFor(
+    'backendRuntime.ackDocumentCleanupEffect'
+  );
+  t.deepEqual(payload, {
+    workspaceId: workspace.id,
+    docId: 'disabled-doc',
+    cleanupVersion: 'version-disabled',
+    effect: 'search',
+  });
+});
+
 test('should handle indexer.deleteWorkspace job', async t => {
   const spy = Sinon.spy(indexerService, 'deleteWorkspace');
 

packages/backend/server/src/plugins/indexer/__tests__/service.spec.ts

@@ -1887,12 +1887,9 @@ test('should delete doc work', async t => {
   t.is(result4.nodes.length, 1);
   t.deepEqual(result4.nodes[0].fields.docId, [docId2]);
 
-  const count = module.queue.count('copilot.embedding.deleteDoc');
-
   await indexerService.deleteDoc(workspaceId, docId1, {
     refresh: true,
   });
-  t.is(module.queue.count('copilot.embedding.deleteDoc'), count + 1);
 
   // make sure the docId1 is deleted
   result1 = await indexerService.search({

packages/backend/server/src/plugins/indexer/index.ts

@@ -3,6 +3,7 @@ import './config';
 import { Module } from '@nestjs/common';
 
 import { ServerConfigModule } from '../../core/config';
+import { DocStorageModule } from '../../core/doc';
 import { PermissionModule } from '../../core/permission';
 import { QuotaServiceModule } from '../../core/quota';
 import { IndexerEvent } from './event';
@@ -13,7 +14,12 @@ import { IndexerResolver } from './resolver';
 import { IndexerService } from './service';
 
 @Module({
-  imports: [ServerConfigModule, PermissionModule, QuotaServiceModule],
+  imports: [
+    ServerConfigModule,
+    DocStorageModule,
+    PermissionModule,
+    QuotaServiceModule,
+  ],
   providers: [
     IndexerResolver,
     IndexerService,

packages/backend/server/src/plugins/indexer/job.ts

@@ -1,6 +1,7 @@
 import { Injectable, Logger } from '@nestjs/common';
 
 import { Config, JOB_SIGNAL, JobQueue, OnJob } from '../../base';
+import { DocReader } from '../../core/doc';
 import { readAllDocIdsFromWorkspaceSnapshot } from '../../core/utils/blocksuite';
 import { Models } from '../../models';
 import { IndexerService } from './service';
@@ -24,6 +25,11 @@ declare global {
     'indexer.autoIndexWorkspaces': {
       lastIndexedWorkspaceSid?: number;
     };
+    'indexer.reconcileDocumentCleanup': {
+      workspaceId: string;
+      docId: string;
+      cleanupVersion: string;
+    };
   }
 }
 
@@ -35,7 +41,8 @@ export class IndexerJob {
     private readonly models: Models,
     private readonly service: IndexerService,
     private readonly queue: JobQueue,
-    private readonly config: Config
+    private readonly config: Config,
+    private readonly doc: DocReader
   ) {}
 
   @OnJob('indexer.indexDoc')
@@ -66,6 +73,39 @@ export class IndexerJob {
     await this.service.deleteDoc(workspaceId, docId);
   }
 
+  @OnJob('indexer.reconcileDocumentCleanup')
+  async reconcileDocumentCleanup({
+    workspaceId,
+    docId,
+    cleanupVersion,
+  }: Jobs['indexer.reconcileDocumentCleanup']) {
+    if (this.config.indexer.enabled) {
+      const root = await this.doc.getDoc(workspaceId, workspaceId);
+      if (!root) {
+        throw new Error(`workspace root ${workspaceId} not found`);
+      }
+      const live = readAllDocIdsFromWorkspaceSnapshot(root.bin, true).includes(
+        docId
+      );
+      if (live) {
+        if (!(await this.doc.getDoc(workspaceId, docId))) {
+          throw new Error(
+            `restored document ${workspaceId}/${docId} not found`
+          );
+        }
+        await this.service.indexDoc(workspaceId, docId);
+      } else {
+        await this.service.deleteDoc(workspaceId, docId);
+      }
+    }
+    await this.queue.add('backendRuntime.ackDocumentCleanupEffect', {
+      workspaceId,
+      docId,
+      cleanupVersion,
+      effect: 'search',
+    });
+  }
+
   @OnJob('indexer.indexWorkspace')
   async indexWorkspace({ workspaceId }: Jobs['indexer.indexWorkspace']) {
     if (!this.config.indexer.enabled) {
@@ -79,16 +119,13 @@ export class IndexerJob {
       return;
     }
 
-    const snapshot = await this.models.doc.getSnapshot(
+    const root = await this.doc.getDoc(workspaceId, workspaceId);
-      workspaceId,
+    if (!root) {
-      workspaceId
-    );
-    if (!snapshot) {
       this.logger.warn(`workspace snapshot ${workspaceId} not found`);
       return;
     }
 
-    const docIdsInWorkspace = readAllDocIdsFromWorkspaceSnapshot(snapshot.blob);
+    const docIdsInWorkspace = readAllDocIdsFromWorkspaceSnapshot(root.bin);
     const docIdsInIndexer = await this.service.listDocIds(workspaceId);
 
     const docIdsInWorkspaceSet = new Set(docIdsInWorkspace);

packages/backend/server/src/plugins/indexer/service.ts

@@ -374,14 +374,6 @@ export class IndexerService {
     );
 
     await this.deleteBlocksByDocId(workspaceId, docId, options);
-    await this.queue.add('copilot.session.deleteDoc', {
-      workspaceId,
-      docId,
-    });
-    await this.queue.add('copilot.embedding.deleteDoc', {
-      workspaceId,
-      docId,
-    });
     this.logger.log(`deleted doc ${workspaceId}/${docId}`);
   }