fix(project-files): persist index completeness across restarts

prisma/schema.prisma

@@ -357,6 +357,13 @@ model ManagedFileSessionSync {
   @@index([projectId, deletedAt, groupSortAtMs, sessionId])
 }
 
+// Singleton completeness marker for catalog-wide Project Files reconciliation. Per-Session retry
+// state remains represented by ManagedFileSessionSync.filesRevision < 0.
+model ManagedFileIndexState {
+  id                       String  @id
+  isReconciliationComplete Boolean @default(true)
+}
+
 // Narrow origin lifecycle retained after a live Session JSON is deleted. This is not a second
 // editable Session model; it exists only to preserve managed-file ownership and deletion state.
 model FileOriginSession {

prisma/sqlite-check-constraints.json

@@ -195,6 +195,11 @@
       "name": "ManagedFile_source_check",
       "expression": "\"source\" IN ('artifact', 'upload')"
     },
+    {
+      "tableName": "ManagedFileIndexState",
+      "name": "ManagedFileIndexState_identity_check",
+      "expression": "\"id\" = 'project-files-index' AND \"isReconciliationComplete\" IN (false, true)"
+    },
     {
       "tableName": "UploadVersion",
       "name": "UploadVersion_state_check",

scripts/ci/module-impact.json

@@ -626,6 +626,7 @@
     },
     "project_files_repository": {
       "ownerPaths": [
+        "src/main/project-files/index-state.ts",
         "src/main/project-files/mutation-owner.ts",
         "src/main/project-files/mutation-projection.ts",
         "src/main/project-files/query-owner.ts",

scripts/database-migration-ledger-smoke.mjs

@@ -80,6 +80,10 @@ const EXPECTED_MIGRATION_LEDGER = [
   {
     id: '0019_session_usage_attribution',
     checksum: 'c505fe7e55e8428d29e8506ad305c04fd46d8def53385a1f7839fba21047ab9d'
+  },
+  {
+    id: '0020_project_files_index_state',
+    checksum: '3db4a30baa2b4614e29205ed56b2682c0579f1a91f5a2d293d21925253ed7fd1'
   }
 ]
 const LEGACY_PROJECT_ID = 'package-smoke-legacy-project'

scripts/database-migration-ledger-smoke.test.ts

@@ -20,7 +20,7 @@ import { PrismaClient } from '@prisma/client'
 describe('packaged database migration ledger smoke', () => {
   it('pins every packaged application migration identity and checksum', () => {
     expect(MIGRATION_MANIFEST.at(-1)?.checksum).toBe(
-      'c505fe7e55e8428d29e8506ad305c04fd46d8def53385a1f7839fba21047ab9d'
+      '3db4a30baa2b4614e29205ed56b2682c0579f1a91f5a2d293d21925253ed7fd1'
     )
     expect(() => assertApplicationMigrationLedger(MIGRATION_MANIFEST)).not.toThrow()
     expect(() => assertApplicationMigrationLedger(MIGRATION_MANIFEST.slice(0, -1))).toThrow(
@@ -93,7 +93,7 @@ describe('packaged database migration ledger smoke', () => {
         'ALTER TABLE "SessionAuxiliaryTurnUsage" DROP COLUMN "providerId"'
       )
       await client.$executeRawUnsafe(
-        `DELETE FROM "_open_science_migrations" WHERE "id" = '0019_session_usage_attribution'`
+        `DELETE FROM "_open_science_migrations" WHERE "id" IN ('0019_session_usage_attribution', '0020_project_files_index_state')`
       )
 
       await migrateApplicationDatabase(client)
@@ -154,7 +154,7 @@ describe('packaged database migration ledger smoke', () => {
       await client.$executeRawUnsafe('DROP INDEX "Review_sessionId_idx"')
       await client.$executeRawUnsafe('DROP INDEX "Finding_reviewId_idx"')
       await client.$executeRawUnsafe(
-        `DELETE FROM "_open_science_migrations" WHERE "id" IN ('0014_review_query_indexes', '0015_session_model_call_usage', '0016_compute_job_sensitive_data_encryption', '0017_agent_memory_project_scope', '0018_session_auxiliary_turn_usage', '0019_session_usage_attribution')`
+        `DELETE FROM "_open_science_migrations" WHERE "id" IN ('0014_review_query_indexes', '0015_session_model_call_usage', '0016_compute_job_sensitive_data_encryption', '0017_agent_memory_project_scope', '0018_session_auxiliary_turn_usage', '0019_session_usage_attribution', '0020_project_files_index_state')`
       )
       await client.$executeRawUnsafe(
         'ALTER TABLE "ComputeJob" DROP COLUMN "sensitiveDataEncrypted"'

src/main/database/agent-memory-project-scope-migration.test.ts

@@ -11,7 +11,8 @@ import { migrateApplicationDatabase, verifyCurrentApplicationSchema } from './mi
 
 const CURRENT_AGENT_MEMORY_MIGRATION_ID = '0017_agent_memory_project_scope'
 const SESSION_AUXILIARY_USAGE_MIGRATION_ID = '0018_session_auxiliary_turn_usage'
-const CURRENT_MIGRATION_ID = '0019_session_usage_attribution'
+const SESSION_USAGE_ATTRIBUTION_MIGRATION_ID = '0019_session_usage_attribution'
+const CURRENT_MIGRATION_ID = '0020_project_files_index_state'
 const MEMORY_AUXILIARY_SCHEMA_NAMES = [
   'MemoryEntryFts',
   'MemoryEntry_fts_insert',
@@ -299,16 +300,18 @@ describe('agent memory project scope migration', () => {
   it('replays an unledgered partial memory migration and restores missing triggers', async () => {
     await client.$executeRawUnsafe('DROP TRIGGER "MemoryEntry_fts_update"')
     await client.$executeRawUnsafe(
-      `DELETE FROM "_open_science_migrations" WHERE "id" IN (?, ?, ?)`,
+      `DELETE FROM "_open_science_migrations" WHERE "id" IN (?, ?, ?, ?)`,
       CURRENT_AGENT_MEMORY_MIGRATION_ID,
       SESSION_AUXILIARY_USAGE_MIGRATION_ID,
+      SESSION_USAGE_ATTRIBUTION_MIGRATION_ID,
       CURRENT_MIGRATION_ID
     )
 
     await expect(migrateApplicationDatabase(client)).resolves.toMatchObject({
       applied: [
         CURRENT_AGENT_MEMORY_MIGRATION_ID,
         SESSION_AUXILIARY_USAGE_MIGRATION_ID,
+        SESSION_USAGE_ATTRIBUTION_MIGRATION_ID,
         CURRENT_MIGRATION_ID
       ],
       to: CURRENT_MIGRATION_ID

src/main/database/application-database.integration.test.ts

@@ -130,7 +130,8 @@ describe('application database (integration)', () => {
         '0016_compute_job_sensitive_data_encryption',
         '0017_agent_memory_project_scope',
         '0018_session_auxiliary_turn_usage',
-        '0019_session_usage_attribution'
+        '0019_session_usage_attribution',
+        '0020_project_files_index_state'
       ]
     })
 
@@ -744,7 +745,7 @@ describe('application database (integration)', () => {
   it('backs up legacy data through the shared client on a portable storage path', async () => {
     storageRoot = await mkdtemp(join(tmpdir(), 'open science 数据 legacy backup-'))
     const databasePath = join(storageRoot, 'open-science.db')
-    const backupPath = `${databasePath}.before-0018_session_auxiliary_turn_usage.backup`
+    const backupPath = `${databasePath}.before-0019_session_usage_attribution.backup`
     const seedClient = createProjectDbClient(storageRoot)
     try {
       await seedClient.$executeRawUnsafe(`CREATE TABLE "Project" (
@@ -784,7 +785,7 @@ describe('application database (integration)', () => {
         backupClient.$queryRaw<Array<{ id: string }>>`
           SELECT "id" FROM "_open_science_migrations" ORDER BY "id" DESC LIMIT 1
         `
-      ).resolves.toEqual([{ id: '0017_agent_memory_project_scope' }])
+      ).resolves.toEqual([{ id: '0018_session_auxiliary_turn_usage' }])
     } finally {
       await backupClient.$disconnect()
     }
@@ -1162,7 +1163,8 @@ describe('application database (integration)', () => {
         '0016_compute_job_sensitive_data_encryption',
         '0017_agent_memory_project_scope',
         '0018_session_auxiliary_turn_usage',
-        '0019_session_usage_attribution'
+        '0019_session_usage_attribution',
+        '0020_project_files_index_state'
       ]
     })
 

src/main/database/compute-job-sensitive-data-encryption-migration.test.ts

@@ -66,10 +66,11 @@ describe('Compute Job sensitive data encryption migration', () => {
         '0016_compute_job_sensitive_data_encryption',
         '0017_agent_memory_project_scope',
         '0018_session_auxiliary_turn_usage',
-        '0019_session_usage_attribution'
+        '0019_session_usage_attribution',
+        '0020_project_files_index_state'
       ],
       from: '0015_session_model_call_usage',
-      to: '0019_session_usage_attribution'
+      to: '0020_project_files_index_state'
     })
     await expect(
       access(`${databasePath}.before-0016_compute_job_sensitive_data_encryption.backup`)
@@ -79,10 +80,13 @@ describe('Compute Job sensitive data encryption migration', () => {
     ).rejects.toMatchObject({ code: 'ENOENT' })
     await expect(
       access(`${databasePath}.before-0018_session_auxiliary_turn_usage.backup`)
-    ).resolves.toBeUndefined()
+    ).rejects.toMatchObject({ code: 'ENOENT' })
     await expect(
       access(`${databasePath}.before-0019_session_usage_attribution.backup`)
     ).resolves.toBeUndefined()
+    await expect(
+      access(`${databasePath}.before-0020_project_files_index_state.backup`)
+    ).resolves.toBeUndefined()
     await expect(
       client.$queryRaw<
         Array<{ command: string; sensitiveDataEncrypted: boolean | null }>

src/main/database/database-json-constraints-migration.test.ts

@@ -158,10 +158,11 @@ describe('database JSON constraints migration', () => {
           '0016_compute_job_sensitive_data_encryption',
           '0017_agent_memory_project_scope',
           '0018_session_auxiliary_turn_usage',
-          '0019_session_usage_attribution'
+          '0019_session_usage_attribution',
+          '0020_project_files_index_state'
         ],
         from: '0007_notification_attention_metadata',
-        to: '0019_session_usage_attribution'
+        to: '0020_project_files_index_state'
       })
       await expect(access(`${databasePath}.before-${MIGRATION_ID}.backup`)).rejects.toMatchObject({
         code: 'ENOENT'
@@ -191,10 +192,13 @@ describe('database JSON constraints migration', () => {
       ).rejects.toMatchObject({ code: 'ENOENT' })
       await expect(
         access(`${databasePath}.before-0018_session_auxiliary_turn_usage.backup`)
-      ).resolves.toBeUndefined()
+      ).rejects.toMatchObject({ code: 'ENOENT' })
       await expect(
         access(`${databasePath}.before-0019_session_usage_attribution.backup`)
       ).resolves.toBeUndefined()
+      await expect(
+        access(`${databasePath}.before-0020_project_files_index_state.backup`)
+      ).resolves.toBeUndefined()
 
       await expect(
         client.$queryRaw<Array<{ scope: string; reviewerLog: string }>>`

src/main/database/database-startup-logging.test.ts

@@ -116,7 +116,8 @@ describe('database startup logging', () => {
               '0016_compute_job_sensitive_data_encryption',
               '0017_agent_memory_project_scope',
               '0018_session_auxiliary_turn_usage',
-              '0019_session_usage_attribution'
+              '0019_session_usage_attribution',
+              '0020_project_files_index_state'
             ],
             adoptedLegacy: true
           })

src/main/database/generated/runtime-schema.ts

@@ -276,6 +276,11 @@ const RUNTIME_SCHEMA_TABLE_DDLS = [
     "deleteOperationId" TEXT,
 
     PRIMARY KEY ("projectId", "sessionId")
+);`,
+  `CREATE TABLE IF NOT EXISTS "ManagedFileIndexState" (
+    "id" TEXT NOT NULL PRIMARY KEY,
+    "isReconciliationComplete" BOOLEAN NOT NULL DEFAULT true,
+    CONSTRAINT "ManagedFileIndexState_identity_check" CHECK ("id" = 'project-files-index' AND "isReconciliationComplete" IN (false, true))
 );`,
   `CREATE TABLE IF NOT EXISTS "FileOriginSession" (
     "projectId" TEXT NOT NULL,
@@ -760,6 +765,7 @@ const RUNTIME_SCHEMA_TABLES = [
   'ProjectDeletionIntent',
   'ManagedFile',
   'ManagedFileSessionSync',
+  'ManagedFileIndexState',
   'FileOriginSession',
   'ArtifactLineage',
   'UploadFile',