fix: preserve knowledge indexing state

src/main/knowledge/knowledge-database.test.ts

@@ -86,7 +86,7 @@ describe('KnowledgeDatabase', () => {
     const inspection = new DatabaseSync(path)
     expect(
       inspection.prepare('PRAGMA user_version').get()
-    ).toEqual({ user_version: 9 })
+    ).toEqual({ user_version: 10 })
     expect(
       inspection
         .prepare('SELECT version FROM schema_migrations ORDER BY version')
@@ -100,7 +100,8 @@ describe('KnowledgeDatabase', () => {
       { version: 6 },
       { version: 7 },
       { version: 8 },
-      { version: 9 }
+      { version: 9 },
+      { version: 10 }
     ])
     inspection.close()
 
@@ -192,7 +193,7 @@ describe('KnowledgeDatabase', () => {
     })
   })
 
-  it('upgrades an existing v1 database through knowledge schema v9', async () => {
+  it('upgrades an existing v1 database through knowledge schema v10', async () => {
     const { database, path } = await createDatabase()
     const knowledgeBase = database.createKnowledgeBase({
       name: 'Version one data',
@@ -208,7 +209,8 @@ describe('KnowledgeDatabase', () => {
       DROP TABLE embedding_index_state;
       DROP TABLE chunk_embeddings;
       DROP TABLE knowledge_tasks;
-      DELETE FROM schema_migrations WHERE version IN (2, 3, 4, 5, 6, 7, 8, 9);
+      DELETE FROM schema_migrations
+      WHERE version IN (2, 3, 4, 5, 6, 7, 8, 9, 10);
       PRAGMA user_version = 1;
     `)
     downgrade.close()
@@ -218,7 +220,7 @@ describe('KnowledgeDatabase', () => {
     upgraded.initialize()
     const inspection = new DatabaseSync(path)
     expect(inspection.prepare('PRAGMA user_version').get()).toEqual({
-      user_version: 9
+      user_version: 10
     })
     expect(
       inspection
@@ -325,7 +327,7 @@ describe('KnowledgeDatabase', () => {
           WHERE new.enabled = 1 AND new.role <> 'parent';
       END;
       INSERT INTO chunks_fts(chunks_fts) VALUES ('rebuild');
-      DELETE FROM schema_migrations WHERE version = 9;
+      DELETE FROM schema_migrations WHERE version IN (9, 10);
       PRAGMA user_version = 8;
     `)
     downgrade
@@ -478,6 +480,38 @@ describe('KnowledgeDatabase', () => {
     ).toMatchObject({ status: 'interrupted', progress: 30 })
   })
 
+  it('bounds task status text from runtime failures', async () => {
+    const { database } = await createDatabase()
+    const library = database.createKnowledgeBase({
+      name: 'Bounded task status',
+      storageMode: 'reference'
+    })
+    const task = database.createKnowledgeTask({
+      libraryId: library.id,
+      documentName: library.name,
+      scope: 'library',
+      kind: 'library-rebuild'
+    })
+
+    expect(
+      database.updateKnowledgeTask(task.id, {
+        status: 'failed',
+        message: 'm'.repeat(2_000),
+        error: {
+          message: 'e'.repeat(2_000),
+          remedy: 'r'.repeat(2_000)
+        }
+      })
+    ).toMatchObject({
+      status: 'failed',
+      message: 'm'.repeat(1_000),
+      error: {
+        message: 'e'.repeat(1_000),
+        remedy: 'r'.repeat(1_000)
+      }
+    })
+  })
+
   it('lists every active task in addition to the terminal history limit', async () => {
     const { database } = await createDatabase()
     const library = database.createKnowledgeBase({
@@ -779,6 +813,63 @@ describe('KnowledgeDatabase', () => {
     expect(database.deleteEntity(other.id)).toBe(true)
   })
 
+  it('finds graph identities beyond the ordinary list limit', async () => {
+    const { database } = await createDatabase()
+    const knowledgeBase = database.createKnowledgeBase({
+      name: 'Large graph identity',
+      storageMode: 'reference'
+    })
+    let expectedEntityId = ''
+    const targetEntityIds: string[] = []
+    for (let index = 0; index < 501; index += 1) {
+      const entity = database.createEntity({
+        knowledgeBaseId: knowledgeBase.id,
+        name: `Entity ${String(index).padStart(3, '0')}`,
+        type: 'CONCEPT',
+        locked: false
+      })
+      targetEntityIds.push(entity.id)
+      if (index === 500) {
+        expectedEntityId = entity.id
+      }
+    }
+    const source = database.createEntity({
+      knowledgeBaseId: knowledgeBase.id,
+      name: 'Relation Source',
+      type: 'CONCEPT',
+      locked: false
+    })
+    let expectedRelationId = ''
+    for (let index = 0; index < 501; index += 1) {
+      const relation = database.createRelation({
+        knowledgeBaseId: knowledgeBase.id,
+        sourceEntityId: source.id,
+        targetEntityId: targetEntityIds[index]!,
+        type: 'RELATED_TO',
+        locked: false
+      })
+      if (index === 500) {
+        expectedRelationId = relation.id
+      }
+    }
+
+    expect(
+      database.findEntityByCanonicalName(
+        knowledgeBase.id,
+        'CONCEPT',
+        'Entity 500'
+      )?.id
+    ).toBe(expectedEntityId)
+    expect(
+      database.findRelationByIdentity(
+        knowledgeBase.id,
+        source.id,
+        targetEntityIds[500]!,
+        'RELATED_TO'
+      )?.id
+    ).toBe(expectedRelationId)
+  })
+
   it('persists controlled ontology updates and marks graph rebuild state', async () => {
     const { database } = await createDatabase()
     const library = database.createKnowledgeBase({
@@ -1229,6 +1320,12 @@ describe('KnowledgeDatabase', () => {
         }
       ]
     )
+    const concurrentReplacementId =
+      database.beginDocumentEmbeddingReplacement(
+        document.id,
+        'openai-compatible',
+        'embed-v1'
+      )
 
     expect(
       database.vectorSearch({
@@ -1244,6 +1341,9 @@ describe('KnowledgeDatabase', () => {
       'openai-compatible',
       'embed-v1'
     )
+    database.discardDocumentEmbeddingReplacement(
+      concurrentReplacementId
+    )
     expect(
       database.vectorSearch({
         knowledgeBaseId: knowledgeBase.id,
@@ -1254,6 +1354,55 @@ describe('KnowledgeDatabase', () => {
     ).toBe(item.id)
   })
 
+  it('rejects a staged embedding replacement after chunk content changes', async () => {
+    const { database } = await createDatabase()
+    const knowledgeBase = database.createKnowledgeBase({
+      name: 'Stale replacement',
+      storageMode: 'reference'
+    })
+    const seeded = seedDocument(
+      database,
+      knowledgeBase.id,
+      'stale-replacement'
+    )
+    const document =
+      database.getEmbeddingIndexDocument(seeded.documentId)!
+    const item = document.items[0]!
+    const replacementId =
+      database.beginDocumentEmbeddingReplacement(
+        document.id,
+        'openai-compatible',
+        'embed-v1'
+      )
+    database.appendDocumentEmbeddingBatch(
+      replacementId,
+      document.id,
+      'openai-compatible',
+      'embed-v1',
+      [{
+        chunkId: item.id,
+        contentChecksum: item.contentChecksum!,
+        vector: [1, 0]
+      }]
+    )
+    database.updateChunk({
+      knowledgeBaseId: knowledgeBase.id,
+      documentId: document.id,
+      chunkId: item.id,
+      content: 'newer content'
+    })
+
+    expect(() =>
+      database.finishDocumentEmbeddingReplacement(
+        replacementId,
+        document.id,
+        'openai-compatible',
+        'embed-v1'
+      )
+    ).toThrow('content changed')
+    database.discardDocumentEmbeddingReplacement(replacementId)
+  })
+
   it('persists embedding index jobs independently by knowledge base', async () => {
     const created = await createDatabase()
     let database = created.database
@@ -1442,6 +1591,20 @@ describe('KnowledgeDatabase', () => {
         0
       ).map((chunk) => chunk.id)
     ).toEqual(['parent-chunk'])
+    const graphEntity = database.createEntity({
+      knowledgeBaseId: library.id,
+      name: 'Chunk evidence',
+      type: 'CONCEPT',
+      locked: false
+    })
+    const evidence = database.createEvidence({
+      knowledgeBaseId: library.id,
+      entityId: graphEntity.id,
+      documentId: document.id,
+      chunkId: 'child-chunk',
+      quote: 'recallable child text',
+      source: 'rules'
+    })
 
     database.updateChunk({
       knowledgeBaseId: library.id,
@@ -1452,6 +1615,12 @@ describe('KnowledgeDatabase', () => {
     expect(
       database.search({ knowledgeBaseId: library.id, query: 'recallable' })
     ).toEqual([])
+    expect(database.listEvidence(library.id)).toEqual([
+      expect.objectContaining({ id: evidence.id })
+    ])
+    expect(
+      database.graphSearch(library.id, 'Chunk evidence')
+    ).toEqual([])
     database.updateChunk({
       knowledgeBaseId: library.id,
       documentId: document.id,
@@ -1462,6 +1631,7 @@ describe('KnowledgeDatabase', () => {
     expect(
       database.search({ knowledgeBaseId: library.id, query: '人工修正' })
     ).toHaveLength(1)
+    expect(database.listEvidence(library.id)).toEqual([])
     expect(
       database.listChunksPage({
         knowledgeBaseId: library.id,

src/main/knowledge/knowledge-database.ts

@@ -45,6 +45,7 @@ import {
   createCjkSearchText,
   knowledgeRetrievalTerms
 } from './retrieval-text'
+import { normalizeEntityAlias } from './graph-extractor'
 import type {
   Chunk,
   ChunkEmbeddingInput,
@@ -79,7 +80,7 @@ import type {
   VectorSearchOptions
 } from './types'
 
-const DATABASE_VERSION = 9
+const DATABASE_VERSION = 10
 const MAX_ID_LENGTH = 128
 const MAX_NAME_LENGTH = 512
 const MAX_LOCATION_LENGTH = 8192
@@ -202,6 +203,17 @@ function optionalString(
   return requiredString(value, field, maximum, trim)
 }
 
+function truncatedOptionalString(
+  value: string | null | undefined,
+  maximum: number
+): string | undefined {
+  if (value === undefined || value === null || value === '') {
+    return undefined
+  }
+  const normalized = String(value).trim()
+  return normalized ? normalized.slice(0, maximum) : undefined
+}
+
 function boundedInteger(
   value: number,
   field: string,
@@ -1340,25 +1352,20 @@ export class KnowledgeDatabase {
         ? undefined
         : update.message === undefined
           ? current.message
-          : optionalString(
-              update.message,
-              'message',
-              MAX_TASK_TEXT_LENGTH
-            )
+          : truncatedOptionalString(update.message, MAX_TASK_TEXT_LENGTH)
     const error =
       update.error === null
         ? undefined
         : update.error === undefined
           ? current.error
           : {
-              message: requiredString(
-                update.error.message,
-                'error.message',
-                MAX_TASK_TEXT_LENGTH
-              ),
-              remedy: optionalString(
+              message:
+                truncatedOptionalString(
+                  update.error.message,
+                  MAX_TASK_TEXT_LENGTH
+                ) ?? '任务失败',
+              remedy: truncatedOptionalString(
                 update.error.remedy,
-                'error.remedy',
                 MAX_TASK_TEXT_LENGTH
               )
             }
@@ -2089,6 +2096,11 @@ export class KnowledgeDatabase {
     const database = this.requireDatabase()
     const now = new Date().toISOString()
     this.transaction(database, () => {
+      if (content !== current.chunk.content) {
+        database
+          .prepare('DELETE FROM graph_evidence WHERE chunk_id = ?')
+          .run(current.chunk.id)
+      }
       database
         .prepare(
           `UPDATE chunks SET content = ?, enabled = ?, manually_edited = 1,
@@ -2110,9 +2122,6 @@ export class KnowledgeDatabase {
       database
         .prepare('DELETE FROM embedding_index_state WHERE document_id = ?')
         .run(current.document.id)
-      database
-        .prepare('DELETE FROM graph_evidence WHERE chunk_id = ?')
-        .run(current.chunk.id)
     })
     return this.getChunkForReference(
       input.knowledgeBaseId,
@@ -2335,12 +2344,12 @@ export class KnowledgeDatabase {
       'documentId',
       MAX_ID_LENGTH
     )
-    const normalizedProvider = requiredString(
+    requiredString(
       provider,
       'provider',
       MAX_EMBEDDING_PROVIDER_LENGTH
     )
-    const normalizedModel = requiredString(
+    requiredString(
       model,
       'model',
       MAX_EMBEDDING_MODEL_LENGTH
@@ -2353,16 +2362,6 @@ export class KnowledgeDatabase {
     ) {
       throw new Error(`Document not found: ${normalizedDocumentId}`)
     }
-    database
-      .prepare(
-        `DELETE FROM embedding_rebuild_staging
-         WHERE document_id = ? AND provider = ? AND model = ?`
-      )
-      .run(
-        normalizedDocumentId,
-        normalizedProvider,
-        normalizedModel
-      )
     return randomUUID()
   }
 
@@ -2544,6 +2543,40 @@ export class KnowledgeDatabase {
     ) {
       throw new Error('Embeddings must cover every current document chunk')
     }
+    const stagedRows = database
+      .prepare(
+        `SELECT
+           staged.content_checksum AS staged_checksum,
+           current.index_content AS current_content
+         FROM embedding_rebuild_staging staged
+         LEFT JOIN chunks current
+           ON current.id = staged.chunk_id
+          AND current.document_id = staged.document_id
+          AND current.enabled = 1
+          AND current.role <> 'parent'
+         WHERE staged.replacement_id = ?
+           AND staged.document_id = ?
+           AND staged.provider = ?
+           AND staged.model = ?`
+      )
+      .all(
+        normalizedReplacementId,
+        normalizedDocumentId,
+        normalizedProvider,
+        normalizedModel
+      )
+    if (
+      stagedRows.some((row) => {
+        const currentContent = asOptionalString(row, 'current_content')
+        return (
+          currentContent === undefined ||
+          asString(row, 'staged_checksum') !==
+            contentChecksum(currentContent)
+        )
+      })
+    ) {
+      throw new Error('Embedding content changed during replacement')
+    }
     const indexHash = createHash('sha256')
     let dimensions: number | undefined
     let firstChecksum = true
@@ -3270,6 +3303,45 @@ export class KnowledgeDatabase {
       .map(mapEntity)
   }
 
+  findEntityByCanonicalName(
+    knowledgeBaseId: string,
+    type: string,
+    name: string
+  ): GraphEntity | undefined {
+    requiredString(knowledgeBaseId, 'knowledgeBaseId', MAX_ID_LENGTH)
+    const normalizedType = requiredString(type, 'type', MAX_NAME_LENGTH)
+    const normalizedName = normalizeEntityAlias(name)
+    if (!normalizedName) {
+      return undefined
+    }
+    return this.listEntitiesForIdentity(knowledgeBaseId)
+      .find(
+        (candidate) =>
+          candidate.type === normalizedType &&
+          (
+            normalizeEntityAlias(candidate.name) === normalizedName ||
+            candidate.aliases.some(
+              (alias) => normalizeEntityAlias(alias) === normalizedName
+            )
+          )
+      )
+  }
+
+  listEntitiesForIdentity(knowledgeBaseId: string): GraphEntity[] {
+    const normalizedId = requiredString(
+      knowledgeBaseId,
+      'knowledgeBaseId',
+      MAX_ID_LENGTH
+    )
+    return this.requireDatabase()
+      .prepare(
+        `SELECT * FROM graph_entities WHERE knowledge_base_id = ?
+         ORDER BY name COLLATE NOCASE ASC, id ASC`
+      )
+      .all(normalizedId)
+      .map(mapEntity)
+  }
+
   updateEntity(id: string, input: UpdateGraphEntityInput): GraphEntity {
     const current = this.requiredEntity(id)
     const ontology =
@@ -3430,6 +3502,32 @@ export class KnowledgeDatabase {
       .map(mapRelation)
   }
 
+  findRelationByIdentity(
+    knowledgeBaseId: string,
+    sourceEntityId: string,
+    targetEntityId: string,
+    type: string
+  ): GraphRelation | undefined {
+    const row = this.requireDatabase()
+      .prepare(
+        `SELECT * FROM graph_relations
+         WHERE knowledge_base_id = ? AND source_entity_id = ?
+           AND target_entity_id = ? AND type = ?
+         ORDER BY created_at ASC, id ASC LIMIT 1`
+      )
+      .get(
+        requiredString(
+          knowledgeBaseId,
+          'knowledgeBaseId',
+          MAX_ID_LENGTH
+        ),
+        requiredString(sourceEntityId, 'sourceEntityId', MAX_ID_LENGTH),
+        requiredString(targetEntityId, 'targetEntityId', MAX_ID_LENGTH),
+        requiredString(type, 'type', MAX_NAME_LENGTH)
+      )
+    return row ? mapRelation(row) : undefined
+  }
+
   updateRelation(
     id: string,
     input: UpdateGraphRelationInput
@@ -3626,6 +3724,42 @@ export class KnowledgeDatabase {
       .map(mapEvidence)
   }
 
+  listGraphSnapshot(knowledgeBaseId: string): {
+    entities: GraphEntity[]
+    relations: GraphRelation[]
+    evidence: Evidence[]
+  } {
+    const normalizedId = requiredString(
+      knowledgeBaseId,
+      'knowledgeBaseId',
+      MAX_ID_LENGTH
+    )
+    const database = this.requireDatabase()
+    return {
+      entities: database
+        .prepare(
+          `SELECT * FROM graph_entities WHERE knowledge_base_id = ?
+           ORDER BY name COLLATE NOCASE ASC, id ASC`
+        )
+        .all(normalizedId)
+        .map(mapEntity),
+      relations: database
+        .prepare(
+          `SELECT * FROM graph_relations WHERE knowledge_base_id = ?
+           ORDER BY created_at ASC, id ASC`
+        )
+        .all(normalizedId)
+        .map(mapRelation),
+      evidence: database
+        .prepare(
+          `SELECT * FROM graph_evidence WHERE knowledge_base_id = ?
+           ORDER BY created_at ASC, id ASC`
+        )
+        .all(normalizedId)
+        .map(mapEvidence)
+    }
+  }
+
   updateEvidence(id: string, input: UpdateEvidenceInput): Evidence {
     const current = this.requiredEvidence(id)
     const next = {
@@ -3961,6 +4095,8 @@ export class KnowledgeDatabase {
                  AND ev.knowledge_base_id = ge.knowledge_base_id
                  AND ec.knowledge_base_id = ge.knowledge_base_id
                  AND ec.document_id = ev.document_id
+                 AND ec.enabled = 1
+                 AND ec.role <> 'parent'
              )
            ORDER BY ge.name COLLATE NOCASE ASC, ge.id ASC
            LIMIT 24
@@ -3988,6 +4124,8 @@ export class KnowledgeDatabase {
                  AND rev.knowledge_base_id = gr.knowledge_base_id
                  AND rc.knowledge_base_id = gr.knowledge_base_id
                  AND rc.document_id = rev.document_id
+                 AND rc.enabled = 1
+                 AND rc.role <> 'parent'
              )
              AND EXISTS (
                SELECT 1 FROM graph_evidence nev
@@ -4000,6 +4138,8 @@ export class KnowledgeDatabase {
                  AND nev.knowledge_base_id = gr.knowledge_base_id
                  AND nc.knowledge_base_id = gr.knowledge_base_id
                  AND nc.document_id = nev.document_id
+                 AND nc.enabled = 1
+                 AND nc.role <> 'parent'
              )
          ),
          reached(id, depth) AS (
@@ -4042,6 +4182,7 @@ export class KnowledgeDatabase {
          JOIN knowledge_sources s ON s.id = d.source_id
          WHERE c.knowledge_base_id = ? AND d.knowledge_base_id = ?
            AND s.knowledge_base_id = ?
+           AND c.enabled = 1 AND c.role <> 'parent'
          GROUP BY c.id
          ORDER BY MIN(backed_evidence.graph_depth) ASC, c.id ASC
          LIMIT ?`
@@ -4175,6 +4316,14 @@ export class KnowledgeDatabase {
           )
           .run(9, new Date().toISOString())
       }
+      if (currentVersion < 10) {
+        this.migrateToVersion10(database)
+        database
+          .prepare(
+            'INSERT INTO schema_migrations (version, applied_at) VALUES (?, ?)'
+          )
+          .run(10, new Date().toISOString())
+      }
       database.exec(`PRAGMA user_version = ${DATABASE_VERSION}`)
       database.exec('COMMIT')
     } catch (error) {
@@ -4783,6 +4932,21 @@ export class KnowledgeDatabase {
     `)
   }
 
+  private migrateToVersion10(database: DatabaseSync): void {
+    database.exec(`
+      CREATE INDEX IF NOT EXISTS graph_evidence_chunk_idx
+        ON graph_evidence(knowledge_base_id, chunk_id);
+      CREATE INDEX IF NOT EXISTS graph_evidence_entity_idx
+        ON graph_evidence(knowledge_base_id, entity_id);
+      CREATE INDEX IF NOT EXISTS graph_evidence_relation_idx
+        ON graph_evidence(knowledge_base_id, relation_id);
+      CREATE INDEX IF NOT EXISTS graph_relations_source_idx
+        ON graph_relations(knowledge_base_id, source_entity_id);
+      CREATE INDEX IF NOT EXISTS graph_relations_target_idx
+        ON graph_relations(knowledge_base_id, target_entity_id);
+    `)
+  }
+
   private normalizeChunks(chunks: ReplaceChunkInput[]): Array<{
     id: string
     ordinal: number

src/main/knowledge/knowledge-service.test.ts

@@ -433,6 +433,37 @@ describe('KnowledgeService', () => {
     expect(service.database.getEntity(manual.id)).toBeDefined()
   })
 
+  it('prunes generated graph records after chunk evidence is removed', async () => {
+    const { directory, service } = await createService()
+    const sourcePath = join(directory, 'chunk-graph.md')
+    await writeFile(sourcePath, '# Disposable Entity', 'utf8')
+    const library = service.createLibrary({
+      name: 'Chunk graph cleanup',
+      storageMode: 'reference',
+      graphEnabled: true,
+      graphStrategy: 'rules'
+    })
+    await service.importPaths(library.id, [sourcePath])
+    const snapshot = service.snapshot(library.id)
+    const document = snapshot.documents[0]!
+    const generatedEntity = snapshot.entities.find(
+      (entity) => entity.name === 'Disposable Entity'
+    )!
+    const evidence = snapshot.evidence.find(
+      (item) => item.entityId === generatedEntity.id
+    )!
+
+    await service.updateChunk({
+      knowledgeBaseId: library.id,
+      documentId: document.id,
+      chunkId: evidence.chunkId!,
+      content: 'Replacement text without graph evidence'
+    })
+
+    expect(service.database.getEntity(generatedEntity.id)).toBeUndefined()
+    expect(service.snapshot(library.id).evidence).toEqual([])
+  })
+
   it('fails hybrid reextraction when model extraction fails', async () => {
     const extractStructured = vi.fn(async () => {
       throw new Error('模型未返回图谱内容')
@@ -633,6 +664,44 @@ describe('KnowledgeService', () => {
     expect(results[0]?.retrieval.channels).toContain('fts')
   })
 
+  it('bounds long indexing failures so task persistence does not mask them', async () => {
+    const directory = await mkdtemp(
+      join(tmpdir(), 'goodbuddy-knowledge-service-')
+    )
+    temporaryDirectories.push(directory)
+    const service = new KnowledgeService({
+      databasePath: join(directory, 'knowledge.sqlite'),
+      managedRoot: join(directory, 'managed'),
+      parseDocument: async () => {
+        throw new Error('x'.repeat(2_000))
+      }
+    })
+    await service.initialize()
+    services.push(service)
+    const sourcePath = join(directory, 'failure.txt')
+    await writeFile(sourcePath, 'failure source', 'utf8')
+    const library = service.createLibrary({
+      name: 'Bounded task errors',
+      storageMode: 'reference',
+      graphEnabled: false
+    })
+
+    await expect(
+      service.importPaths(library.id, [sourcePath])
+    ).rejects.toThrow()
+    const failedTasks = service
+      .snapshot(library.id)
+      .tasks.filter((task) => task.status === 'failed')
+    expect(failedTasks.length).toBeGreaterThan(0)
+    expect(
+      failedTasks.every(
+        (task) =>
+          (task.message?.length ?? 0) <= 1_000 &&
+          (task.error?.message.length ?? 0) <= 1_000
+      )
+    ).toBe(true)
+  })
+
   it('defers existing-document rebuilds when an embedding provider is enabled', async () => {
     const { directory, service } = await createService()
     const sourcePath = join(directory, 'existing.txt')
@@ -1202,6 +1271,149 @@ describe('KnowledgeService', () => {
     })
   })
 
+  it('marks an existing URL source failed when refresh fails before parsing', async () => {
+    const importer = {
+      import: vi.fn(async () => {
+        throw new Error('URL refresh unavailable')
+      })
+    } as unknown as UrlImporter
+    const { service } = await createService(importer)
+    const library = service.createLibrary({
+      name: 'Failed URL refresh',
+      storageMode: 'managed',
+      graphEnabled: false
+    })
+    const source = service.database.upsertSource({
+      knowledgeBaseId: library.id,
+      type: 'url',
+      location: 'https://example.com/failure',
+      displayName: 'Existing URL',
+      status: 'ready'
+    })
+
+    await expect(service.syncSource(source.id)).rejects.toThrow(
+      'URL refresh unavailable'
+    )
+    expect(service.database.getSource(source.id)).toMatchObject({
+      status: 'error',
+      lastError: 'URL refresh unavailable'
+    })
+  })
+
+  it('preserves refreshed URL metadata when later indexing fails', async () => {
+    const importer = {
+      import: vi.fn(async () => ({
+        url: 'https://example.com/redirected',
+        title: 'Redirected title',
+        contentType: 'text/html',
+        etag: 'fresh-etag',
+        lastModified: undefined,
+        discoveredUrls: [],
+        document: {
+          title: 'Redirected title',
+          sourceFormat: '.html',
+          content: 'refreshed content',
+          sections: [{
+            locator: '网页正文',
+            content: 'refreshed content'
+          }],
+          warnings: []
+        }
+      }))
+    } as unknown as UrlImporter
+    const { service } = await createService(importer)
+    const library = service.createLibrary({
+      name: 'Failed refreshed URL',
+      storageMode: 'managed',
+      graphEnabled: false
+    })
+    const source = service.database.upsertSource({
+      knowledgeBaseId: library.id,
+      type: 'url',
+      location: 'https://example.com/original',
+      displayName: 'Original title',
+      status: 'ready'
+    })
+    vi.spyOn(service.database, 'upsertDocument').mockImplementationOnce(
+      () => {
+        throw new Error('synthetic indexing failure')
+      }
+    )
+
+    await expect(service.syncSource(source.id)).rejects.toThrow(
+      'synthetic indexing failure'
+    )
+    expect(service.database.getSource(source.id)).toMatchObject({
+      location: 'https://example.com/redirected',
+      displayName: 'Redirected title',
+      status: 'error',
+      metadata: expect.objectContaining({ etag: 'fresh-etag' })
+    })
+  })
+
+  it('serializes background embedding reindexes and awaits the rerun on disposal', async () => {
+    const resolvers: Array<() => void> = []
+    let activeEmbeddings = 0
+    let maximumActiveEmbeddings = 0
+    const provider: EmbeddingProvider = {
+      provider: 'serial-background-provider',
+      model: 'serial-background-model',
+      embed: vi.fn(async () => {
+        activeEmbeddings += 1
+        maximumActiveEmbeddings = Math.max(
+          maximumActiveEmbeddings,
+          activeEmbeddings
+        )
+        await new Promise<void>((resolve) => {
+          resolvers.push(resolve)
+        })
+        activeEmbeddings -= 1
+        return [[1, 0]]
+      })
+    }
+    const { directory, service } = await createService()
+    const sourcePath = join(directory, 'serial-background.txt')
+    await writeFile(sourcePath, 'initial content', 'utf8')
+    const library = service.createLibrary({
+      name: 'Serialized background embeddings',
+      storageMode: 'reference',
+      graphEnabled: false
+    })
+    await service.importPaths(library.id, [sourcePath])
+    await service.setEmbeddingProvider(provider)
+    const document = service.snapshot(library.id).documents[0]!
+    const chunk = service.database.listChunks(document.id, 1)[0]!
+
+    await service.updateChunk({
+      knowledgeBaseId: library.id,
+      documentId: document.id,
+      chunkId: chunk.id,
+      content: 'first edit'
+    })
+    await vi.waitFor(() => expect(resolvers).toHaveLength(1))
+    await service.updateChunk({
+      knowledgeBaseId: library.id,
+      documentId: document.id,
+      chunkId: chunk.id,
+      content: 'second edit'
+    })
+    await new Promise((resolve) => setTimeout(resolve, 300))
+    expect(maximumActiveEmbeddings).toBe(1)
+
+    resolvers.shift()?.()
+    await vi.waitFor(() => expect(resolvers).toHaveLength(1))
+    const disposing = service.dispose()
+    let disposed = false
+    void disposing.then(() => {
+      disposed = true
+    })
+    await new Promise((resolve) => setTimeout(resolve, 0))
+    expect(disposed).toBe(false)
+    resolvers.shift()?.()
+    await disposing
+    expect(maximumActiveEmbeddings).toBe(1)
+  })
+
   it('cancels and awaits active graph work before deleting a library', async () => {
     let extractionSignal: AbortSignal | undefined
     const extractStructured: ExtractStructured = (_prompt, signal) => {
@@ -1280,6 +1492,54 @@ describe('KnowledgeService', () => {
     ).toBe(true)
   })
 
+  it('deduplicates a source retry against an active manual sync', async () => {
+    let releaseImport: (() => void) | undefined
+    const importer = {
+      import: vi.fn(
+        async () => {
+          await new Promise<void>((resolve) => {
+            releaseImport = resolve
+          })
+          throw new Error('synthetic sync failure')
+        }
+      )
+    } as unknown as UrlImporter
+    const { service } = await createService(importer)
+    const library = service.createLibrary({
+      name: 'Dedupe source retry',
+      storageMode: 'managed',
+      graphEnabled: false
+    })
+    const source = service.database.upsertSource({
+      knowledgeBaseId: library.id,
+      type: 'url',
+      location: 'https://example.com/dedupe',
+      displayName: 'Dedupe URL',
+      status: 'ready'
+    })
+    const failed = service.database.createKnowledgeTask({
+      libraryId: library.id,
+      sourceId: source.id,
+      documentName: source.displayName,
+      scope: 'source',
+      kind: 'source-sync',
+      status: 'failed',
+      error: { message: 'retry me' }
+    })
+
+    const syncing = service.syncSource(source.id)
+    void syncing.catch(() => undefined)
+    await vi.waitFor(() => expect(importer.import).toHaveBeenCalledOnce())
+    const retrying = service.retryTask(failed.id)
+    void retrying.catch(() => undefined)
+    await new Promise((resolve) => setTimeout(resolve, 0))
+    expect(importer.import).toHaveBeenCalledOnce()
+
+    releaseImport?.()
+    await expect(syncing).rejects.toThrow('synthetic sync failure')
+    await expect(retrying).rejects.toThrow('synthetic sync failure')
+  })
+
   it('reconciles embedding task status during ordinary snapshots', async () => {
     let resolveEmbedding: ((value: number[][]) => void) | undefined
     const provider: EmbeddingProvider = {

src/main/knowledge/knowledge-service.ts

@@ -2,7 +2,6 @@ import {
   cp,
   lstat,
   mkdir,
-  open,
   readdir,
   realpath,
   rm,
@@ -91,7 +90,10 @@ import type {
 } from './types'
 import { UrlImporter } from './url-importer'
 import { mimeTypeFromFileName } from '../file-media-type'
-import { isPathInside } from '../workspace-file-access'
+import {
+  isPathInside,
+  readBoundedFile
+} from '../workspace-file-access'
 
 type ScannedFile = {
   absolutePath: string
@@ -182,6 +184,11 @@ export class KnowledgeService {
     string,
     Promise<Document>
   >()
+  private readonly backgroundEmbeddingReindexes = new Map<
+    string,
+    Promise<void>
+  >()
+  private readonly pendingEmbeddingReindexes = new Set<string>()
   private readonly taskControllers = new Map<string, AbortController>()
   private readonly taskOperations = new Map<string, Promise<unknown>>()
   private readonly sourceSyncTaskIds = new Map<string, string>()
@@ -253,6 +260,7 @@ export class KnowledgeService {
       clearTimeout(timer)
     }
     this.embeddingEditTimers.clear()
+    this.pendingEmbeddingReindexes.clear()
     for (const watcher of this.watchers.values()) {
       watcher.close()
     }
@@ -266,6 +274,7 @@ export class KnowledgeService {
     await Promise.allSettled([
       ...this.activeSyncs.values(),
       ...this.activeDocumentRebuilds.values(),
+      ...this.backgroundEmbeddingReindexes.values(),
       ...this.taskOperations.values(),
       ...embeddingCompletions
     ])
@@ -451,6 +460,11 @@ export class KnowledgeService {
     })
   }
 
+  private static taskErrorMessage(error: unknown): string {
+    const message = error instanceof Error ? error.message : '任务失败'
+    return message.slice(0, 1_000) || '任务失败'
+  }
+
   private failKnowledgeTask(taskId: string, error: unknown): void {
     const current = this.database.getKnowledgeTask(taskId)
     if (
@@ -459,7 +473,7 @@ export class KnowledgeService {
     ) {
       return
     }
-    const message = error instanceof Error ? error.message : '任务失败'
+    const message = KnowledgeService.taskErrorMessage(error)
     this.database.updateKnowledgeTask(taskId, {
       status: 'failed',
       message,
@@ -712,13 +726,14 @@ export class KnowledgeService {
             : undefined
       }
     })
+    const graph = this.database.listGraphSnapshot(libraryId)
     return {
       libraries,
       sources,
       documents,
-      entities: this.database.listEntities(libraryId),
-      relations: this.database.listRelations(libraryId),
-      evidence: this.database.listEvidence(libraryId),
+      entities: graph.entities,
+      relations: graph.relations,
+      evidence: graph.evidence,
       tasks: this.database.listKnowledgeTasks(libraryId)
     }
   }
@@ -1223,6 +1238,15 @@ export class KnowledgeService {
     ) {
       this.scheduleEmbeddingReindex(input.documentId)
     }
+    if (
+      current &&
+      input.content !== undefined &&
+      input.content !== current.content
+    ) {
+      this.database.pruneUnreferencedGeneratedGraph(
+        input.knowledgeBaseId
+      )
+    }
     return chunk
   }
 
@@ -1231,6 +1255,9 @@ export class KnowledgeService {
     const deleted = this.database.deleteChunk(input)
     if (deleted) {
       this.scheduleEmbeddingReindex(input.documentId)
+      this.database.pruneUnreferencedGeneratedGraph(
+        input.knowledgeBaseId
+      )
     }
     return deleted
   }
@@ -1618,6 +1645,7 @@ export class KnowledgeService {
             effectiveLibrary
           )
         )
+        this.database.pruneUnreferencedGeneratedGraph(library.id)
         this.updateKnowledgeTask(parsingTask.id, {
           documentId: document.id,
           documentName: document.title,
@@ -1702,11 +1730,21 @@ export class KnowledgeService {
   }
 
   async syncSource(sourceId: string): Promise<void> {
+    return this.syncSourceOperation(sourceId)
+  }
+
+  private async syncSourceOperation(
+    sourceId: string,
+    retryOfTaskId?: string
+  ): Promise<void> {
     const existing = this.activeSyncs.get(sourceId)
     if (existing) {
       return existing
     }
-    const operation = this.performSyncSource(sourceId).finally(() => {
+    const operation = this.performSyncSource(
+      sourceId,
+      retryOfTaskId
+    ).finally(() => {
       if (this.activeSyncs.get(sourceId) === operation) {
         this.activeSyncs.delete(sourceId)
       }
@@ -1836,7 +1874,12 @@ export class KnowledgeService {
         progress: 5,
         message: '正在读取文档'
       })
-      const buffer = await this.readBoundedFile(location)
+      const buffer = await readBoundedFile(
+        location,
+        maximumFileBytes,
+        '文件超过 20MB',
+        '文件不是普通文件'
+      )
       effectiveSignal.throwIfAborted()
       this.updateKnowledgeTask(task.id, {
         stage: 'parsing',
@@ -1868,6 +1911,7 @@ export class KnowledgeService {
         },
         this.createDocumentChunks(parsed, library)
       )
+      this.database.pruneUnreferencedGeneratedGraph(library.id)
       this.updateKnowledgeTask(task.id, {
         stage: 'embedding',
         progress: 65,
@@ -2073,7 +2117,7 @@ export class KnowledgeService {
         if (!task.sourceId) {
           throw new Error('任务缺少知识来源')
         }
-        await this.performSyncSource(task.sourceId, task.id)
+        await this.syncSourceOperation(task.sourceId, task.id)
         return
       }
       case 'document-rebuild': {
@@ -2151,7 +2195,8 @@ export class KnowledgeService {
     if (library.graphStrategy === 'ask') {
       throw new Error('按需询问策略不会自动抽取，请在设置中选择其他策略')
     }
-    const documents = this.database.listDocuments(library.id)
+    const documents =
+      this.database.listDocumentsForLibraryRebuild(library.id)
     const parentTask = this.createKnowledgeTask({
       libraryId: library.id,
       retryOfTaskId,
@@ -2293,6 +2338,9 @@ export class KnowledgeService {
       'Knowledge source deleted'
     )
     const removed = this.database.removeSource(sourceId)
+    if (removed) {
+      this.database.pruneUnreferencedGeneratedGraph(library.id)
+    }
     if (
       removed &&
       library.storageMode === 'managed' &&
@@ -2395,13 +2443,18 @@ export class KnowledgeService {
       } else {
         this.failKnowledgeTask(task.id, error)
       }
-      if (!effectiveSignal.aborted && source.type !== 'url') {
-        this.database.upsertSource({
-          ...source,
-          status: 'error',
-          lastError:
-            error instanceof Error ? error.message.slice(0, 1_000) : '同步失败'
-        })
+      if (!effectiveSignal.aborted) {
+        const currentSource = this.database.getSource(source.id)
+        if (currentSource) {
+          this.database.upsertSource({
+            ...currentSource,
+            status: 'error',
+            lastError:
+              error instanceof Error
+                ? error.message.slice(0, 1_000)
+                : '同步失败'
+          })
+        }
       }
       throw error
     } finally {
@@ -2431,6 +2484,11 @@ export class KnowledgeService {
         this.database.removeDocument(document.id)
       }
     }
+    if (existing.some(
+      (document) => !currentExternalIds.has(document.externalId)
+    )) {
+      this.database.pruneUnreferencedGeneratedGraph(library.id)
+    }
 
     const failures: string[] = []
     for (let index = 0; index < files.length; index += 1) {
@@ -2454,7 +2512,12 @@ export class KnowledgeService {
           progress: 10,
           message: '正在读取文档'
         })
-        const buffer = await this.readBoundedFile(file.absolutePath)
+        const buffer = await readBoundedFile(
+          file.absolutePath,
+          maximumFileBytes,
+          '文件超过 20MB',
+          '文件不是普通文件'
+        )
         signal.throwIfAborted()
         this.updateKnowledgeTask(parsingTask.id, {
           stage: 'parsing',
@@ -2507,6 +2570,7 @@ export class KnowledgeService {
           },
           this.createDocumentChunks(parsed, effectiveLibrary)
         )
+        this.database.pruneUnreferencedGeneratedGraph(library.id)
         this.updateKnowledgeTask(parsingTask.id, {
           documentId: document.id,
           documentName: document.title,
@@ -2550,7 +2614,7 @@ export class KnowledgeService {
         this.failKnowledgeTask(parsingTask.id, error)
         failures.push(
           `${file.relativePath}: ${
-            error instanceof Error ? error.message : '解析失败'
+            KnowledgeService.taskErrorMessage(error)
           }`
         )
       }
@@ -2564,8 +2628,9 @@ export class KnowledgeService {
       })
     }
     if (failures.length > 0) {
+      const detail = failures.slice(0, 5).join('；')
       throw new Error(
-        `${failures.length} 个文件处理失败：${failures.slice(0, 5).join('；')}`
+        `${failures.length} 个文件处理失败：${detail}`.slice(0, 1_000)
       )
     }
   }
@@ -2577,15 +2642,49 @@ export class KnowledgeService {
     }
     const timer = setTimeout(() => {
       this.embeddingEditTimers.delete(documentId)
-      const document = this.database.getDocument(documentId)
-      if (document && this.embeddingProvider) {
-        void this.indexDocumentEmbeddings(document)
+      if (this.backgroundEmbeddingReindexes.has(documentId)) {
+        this.pendingEmbeddingReindexes.add(documentId)
+        return
       }
+      this.startBackgroundEmbeddingReindex(documentId)
     }, 250)
     timer.unref?.()
     this.embeddingEditTimers.set(documentId, timer)
   }
 
+  private startBackgroundEmbeddingReindex(documentId: string): void {
+    if (
+      this.backgroundEmbeddingReindexes.has(documentId) ||
+      this.lifecycleController.signal.aborted
+    ) {
+      return
+    }
+    const operation = (async () => {
+      do {
+        this.pendingEmbeddingReindexes.delete(documentId)
+        const document = this.database.getDocument(documentId)
+        if (
+          !document ||
+          !this.embeddingProvider ||
+          this.lifecycleController.signal.aborted
+        ) {
+          return
+        }
+        await this.indexDocumentEmbeddings(document)
+      } while (this.pendingEmbeddingReindexes.delete(documentId))
+    })()
+      .catch(() => undefined)
+      .finally(() => {
+        this.pendingEmbeddingReindexes.delete(documentId)
+        if (
+          this.backgroundEmbeddingReindexes.get(documentId) === operation
+        ) {
+          this.backgroundEmbeddingReindexes.delete(documentId)
+        }
+      })
+    this.backgroundEmbeddingReindexes.set(documentId, operation)
+  }
+
   private cancelScheduledEmbeddingReindex(documentId: string): void {
     const timer = this.embeddingEditTimers.get(documentId)
     if (timer) {
@@ -2850,23 +2949,24 @@ export class KnowledgeService {
     document: Document,
     result: GraphExtractionResult
   ): void {
-    const existingEntities = this.database.listEntities(library.id)
     const chunksById = new Map(
       this.database
         .listChunks(document.id)
         .map((chunk) => [chunk.id, chunk])
     )
     const entityIds = new Map<string, string>()
+    const existingEntitiesByIdentity = new Map<string, GraphEntity>()
+    for (const entity of this.database.listEntitiesForIdentity(library.id)) {
+      for (const name of [entity.name, ...entity.aliases]) {
+        existingEntitiesByIdentity.set(
+          `${entity.type}\0${normalizeEntityAlias(name)}`,
+          entity
+        )
+      }
+    }
     for (const entity of result.entities) {
-      const normalized = normalizeEntityAlias(entity.name)
-      const existing = existingEntities.find(
-        (candidate) =>
-          candidate.type === entity.type &&
-          (normalizeEntityAlias(candidate.name) === normalized ||
-            candidate.aliases.some(
-              (alias) => normalizeEntityAlias(alias) === normalized
-            ))
-      )
+      const identity = `${entity.type}\0${normalizeEntityAlias(entity.name)}`
+      const existing = existingEntitiesByIdentity.get(identity)
       const stored = existing
         ? existing.locked
           ? existing
@@ -2880,6 +2980,12 @@ export class KnowledgeService {
             aliases: entity.aliases,
             locked: false
           })
+      for (const name of [stored.name, ...stored.aliases]) {
+        existingEntitiesByIdentity.set(
+          `${stored.type}\0${normalizeEntityAlias(name)}`,
+          stored
+        )
+      }
       entityIds.set(entity.id, stored.id)
       for (const evidence of entity.evidence) {
         this.database.createEvidence({
@@ -2900,18 +3006,17 @@ export class KnowledgeService {
         })
       }
     }
-    const existingRelations = this.database.listRelations(library.id)
     for (const relation of result.relations) {
       const sourceEntityId = entityIds.get(relation.sourceId)
       const targetEntityId = entityIds.get(relation.targetId)
       if (!sourceEntityId || !targetEntityId) {
         continue
       }
-      const existing = existingRelations.find(
-        (candidate) =>
-          candidate.sourceEntityId === sourceEntityId &&
-          candidate.targetEntityId === targetEntityId &&
-          candidate.type === relation.type
+      const existing = this.database.findRelationByIdentity(
+        library.id,
+        sourceEntityId,
+        targetEntityId,
+        relation.type
       )
       const stored =
         existing ??
@@ -3027,24 +3132,6 @@ export class KnowledgeService {
     }
   }
 
-  private async readBoundedFile(path: string): Promise<Buffer> {
-    const handle = await open(path, 'r')
-    try {
-      const fileStat = await handle.stat()
-      if (!fileStat.isFile() || fileStat.size > maximumFileBytes) {
-        throw new Error('文件超过 20MB 或不是普通文件')
-      }
-      const buffer = Buffer.alloc(fileStat.size + 1)
-      const result = await handle.read(buffer, 0, buffer.length, 0)
-      if (result.bytesRead > maximumFileBytes) {
-        throw new Error('文件超过 20MB')
-      }
-      return buffer.subarray(0, result.bytesRead)
-    } finally {
-      await handle.close()
-    }
-  }
-
   private startWatcher(source: KnowledgeSource): void {
     this.stopWatcher(source.id)
     try {