rag-rat-core 0.3.1

Repository evidence engine for source chunks, symbols, graph edges, Git history, GitHub rationale, and source-bound memories.
Documentation
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
use rusqlite::{Connection, OptionalExtension, params};
use serde::Serialize;

pub const LATEST_SCHEMA_VERSION: u32 = 13;
const DIRTY_MIGRATION_ID: &str = "__dirty__";
const MIGRATION_001_ID: &str = "001_sqlite_storage_baseline";
const MIGRATION_001_CHECKSUM: &str = "sha256:rag-rat-sqlite-baseline-v1";
const MIGRATION_001_DESCRIPTION: &str =
    "SQLite storage baseline with FTS, tree-sitter graph edges, git/GitHub, and local AI metadata";
const MIGRATION_002_ID: &str = "002_embedding_vector_metadata";
const MIGRATION_002_CHECKSUM: &str = "sha256:rag-rat-embedding-vector-metadata-v2";
const MIGRATION_002_DESCRIPTION: &str =
    "Add embedding model dimension metadata and per-vector dimensions for hybrid vector search";
const MIGRATION_003_ID: &str = "003_derived_artifact_reconcile_metadata";
const MIGRATION_003_CHECKSUM: &str = "sha256:rag-rat-derived-artifact-reconcile-metadata-v3";
const MIGRATION_003_DESCRIPTION: &str = "Add model version, retry metadata, summaries, and reconcile meta for diff-based derived artifact reconciliation";
const MIGRATION_004_ID: &str = "004_edge_source_target_spans";
const MIGRATION_004_CHECKSUM: &str = "sha256:rag-rat-edge-source-target-spans-v4";
const MIGRATION_004_DESCRIPTION: &str =
    "Add exact source call-site spans and resolved target line spans to graph edges";
const MIGRATION_005_ID: &str = "005_edge_evidence_and_resolution";
const MIGRATION_005_CHECKSUM: &str = "sha256:rag-rat-edge-evidence-resolution-v5";
const MIGRATION_005_DESCRIPTION: &str =
    "Add raw graph edge evidence, receiver hints, qualified targets, and resolution reasons";
const MIGRATION_006_ID: &str = "006_embedding_policy_and_input_hash";
const MIGRATION_006_CHECKSUM: &str = "sha256:rag-rat-embedding-policy-input-hash-v6";
const MIGRATION_006_DESCRIPTION: &str = "Add embedding eligibility policy, priority, bounded input hash, and reconcile throughput metadata";
const MIGRATION_007_ID: &str = "007_logical_symbol_groups";
const MIGRATION_007_CHECKSUM: &str = "sha256:rag-rat-logical-symbol-groups-v7";
const MIGRATION_007_DESCRIPTION: &str =
    "Add logical symbol groups for cfg variants and duplicate definitions";
const MIGRATION_008_ID: &str = "008_commit_addressable_worktrees";
const MIGRATION_008_CHECKSUM: &str = "sha256:rag-rat-commit-addressable-worktrees-v8";
const MIGRATION_008_DESCRIPTION: &str =
    "Add commit_sha and worktree_id to files table for multi-worktree / multi-branch support";
const MIGRATION_009_ID: &str = "009_github_ref_sync_state";
const MIGRATION_009_CHECKSUM: &str = "sha256:rag-rat-github-ref-sync-state-v9";
const MIGRATION_009_DESCRIPTION: &str =
    "Add per-GitHub-ref sync state for resumable papertrail cache updates";
const MIGRATION_010_ID: &str = "010_symbol_facts";
const MIGRATION_010_CHECKSUM: &str = "sha256:rag-rat-symbol-facts-v10";
const MIGRATION_010_DESCRIPTION: &str =
    "Add normalized symbol facts for parsed language metadata such as Rust attributes";
const MIGRATION_011_ID: &str = "011_repo_memories";
const MIGRATION_011_CHECKSUM: &str = "sha256:rag-rat-repo-memories-v11";
const MIGRATION_011_DESCRIPTION: &str =
    "Add source-anchored repo memories bound to symbols, chunks, paths, and papertrail refs";
const MIGRATION_012_ID: &str = "012_repo_memory_call_paths";
const MIGRATION_012_CHECKSUM: &str = "sha256:rag-rat-repo-memory-call-paths-v12";
const MIGRATION_012_DESCRIPTION: &str =
    "Add edge and call-path memory bindings for graph traversal surfacing";
const MIGRATION_013_ID: &str = "013_graph_file_lookup_indexes";
const MIGRATION_013_CHECKSUM: &str = "sha256:rag-rat-graph-file-lookup-indexes-v13";
const MIGRATION_013_DESCRIPTION: &str =
    "Add graph file lookup indexes for ownership clustering and file-level graph summaries";

#[derive(Debug, Clone, Serialize, PartialEq, Eq)]
#[serde(rename_all = "snake_case")]
pub enum SchemaState {
    Missing,
    Compatible,
    Older,
    Newer,
    Dirty,
}

#[derive(Debug, Clone, Serialize)]
pub struct AppliedMigration {
    pub id: String,
    pub applied_at_ms: i64,
    pub checksum: String,
    pub description: String,
}

#[derive(Debug, Clone, Serialize)]
pub struct SchemaStatus {
    pub state: SchemaState,
    pub current_version: u32,
    pub latest_version: u32,
    pub migrations: Vec<AppliedMigration>,
    pub message: String,
}

pub fn apply(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS schema_version(
            id TEXT PRIMARY KEY,
            applied_at_ms INTEGER NOT NULL,
            checksum TEXT NOT NULL,
            description TEXT NOT NULL
        );
        ",
    )?;
    conn.execute(
        "INSERT OR REPLACE INTO schema_version(id, applied_at_ms, checksum, description)
         VALUES (?1, ?2, ?3, ?4)",
        params![DIRTY_MIGRATION_ID, now_ms(), "", "partial migration in progress"],
    )?;
    let result = apply_baseline(conn);
    if let Err(err) = result {
        let _ = conn.execute(
            "UPDATE schema_version SET description = ?2 WHERE id = ?1",
            params![DIRTY_MIGRATION_ID, format!("partial migration failed: {err}")],
        );
        return Err(err);
    }
    conn.execute("DELETE FROM schema_version WHERE id = ?1", [DIRTY_MIGRATION_ID])?;
    record_migration(conn, MIGRATION_001_ID, MIGRATION_001_CHECKSUM, MIGRATION_001_DESCRIPTION)?;
    apply_embedding_vector_metadata(conn)?;
    record_migration(conn, MIGRATION_002_ID, MIGRATION_002_CHECKSUM, MIGRATION_002_DESCRIPTION)?;
    apply_derived_artifact_reconcile_metadata(conn)?;
    record_migration(conn, MIGRATION_003_ID, MIGRATION_003_CHECKSUM, MIGRATION_003_DESCRIPTION)?;
    apply_edge_source_target_spans(conn)?;
    record_migration(conn, MIGRATION_004_ID, MIGRATION_004_CHECKSUM, MIGRATION_004_DESCRIPTION)?;
    apply_edge_evidence_and_resolution(conn)?;
    record_migration(conn, MIGRATION_005_ID, MIGRATION_005_CHECKSUM, MIGRATION_005_DESCRIPTION)?;
    apply_embedding_policy_and_input_hash(conn)?;
    record_migration(conn, MIGRATION_006_ID, MIGRATION_006_CHECKSUM, MIGRATION_006_DESCRIPTION)?;
    apply_logical_symbol_groups(conn)?;
    record_migration(conn, MIGRATION_007_ID, MIGRATION_007_CHECKSUM, MIGRATION_007_DESCRIPTION)?;
    apply_commit_addressable_worktrees(conn)?;
    record_migration(conn, MIGRATION_008_ID, MIGRATION_008_CHECKSUM, MIGRATION_008_DESCRIPTION)?;
    apply_github_ref_sync(conn)?;
    record_migration(conn, MIGRATION_009_ID, MIGRATION_009_CHECKSUM, MIGRATION_009_DESCRIPTION)?;
    apply_symbol_facts(conn)?;
    record_migration(conn, MIGRATION_010_ID, MIGRATION_010_CHECKSUM, MIGRATION_010_DESCRIPTION)?;
    apply_repo_memories(conn)?;
    record_migration(conn, MIGRATION_011_ID, MIGRATION_011_CHECKSUM, MIGRATION_011_DESCRIPTION)?;
    apply_repo_memory_call_paths(conn)?;
    record_migration(conn, MIGRATION_012_ID, MIGRATION_012_CHECKSUM, MIGRATION_012_DESCRIPTION)?;
    apply_graph_file_lookup_indexes(conn)?;
    record_migration(conn, MIGRATION_013_ID, MIGRATION_013_CHECKSUM, MIGRATION_013_DESCRIPTION)?;
    Ok(())
}

pub fn status(conn: &Connection) -> anyhow::Result<SchemaStatus> {
    if !table_exists(conn, "schema_version")? {
        let has_legacy_tables = table_exists(conn, "files")? || table_exists(conn, "chunks")?;
        return Ok(if has_legacy_tables {
            SchemaStatus {
                state: SchemaState::Older,
                current_version: 0,
                latest_version: LATEST_SCHEMA_VERSION,
                migrations: Vec::new(),
                message: "legacy index schema has no schema_version table; run `rag-rat migrate` or rebuild the derived index with `rag-rat index --full`".to_string(),
            }
        } else {
            SchemaStatus {
                state: SchemaState::Missing,
                current_version: 0,
                latest_version: LATEST_SCHEMA_VERSION,
                migrations: Vec::new(),
                message: "index schema is not initialized; run `rag-rat migrate` or build the derived index with `rag-rat index --full`".to_string(),
            }
        });
    }

    let migrations = applied_migrations(conn)?;
    if migrations.iter().any(|migration| migration.id == DIRTY_MIGRATION_ID) {
        return Ok(SchemaStatus {
            state: SchemaState::Dirty,
            current_version: known_version(&migrations),
            latest_version: LATEST_SCHEMA_VERSION,
            migrations,
            message: "dirty or partial schema migration detected; rebuild the derived index with `rag-rat index --full`".to_string(),
        });
    }
    if migrations.iter().any(migration_checksum_mismatch) {
        return Ok(SchemaStatus {
            state: SchemaState::Dirty,
            current_version: known_version(&migrations),
            latest_version: LATEST_SCHEMA_VERSION,
            migrations,
            message: "schema migration checksum mismatch; refusing to open, rebuild the derived index with `rag-rat index --full`".to_string(),
        });
    }
    if migrations.iter().any(|migration| !known_migration(&migration.id)) {
        return Ok(SchemaStatus {
            state: SchemaState::Newer,
            current_version: known_version(&migrations),
            latest_version: LATEST_SCHEMA_VERSION,
            migrations,
            message: "index schema was created by a newer rag-rat; refusing to open".to_string(),
        });
    }
    let current_version = known_version(&migrations);
    if current_version < LATEST_SCHEMA_VERSION {
        return Ok(SchemaStatus {
            state: SchemaState::Older,
            current_version,
            latest_version: LATEST_SCHEMA_VERSION,
            migrations,
            message: "index schema is older than this rag-rat; run `rag-rat migrate` or rebuild the derived index with `rag-rat index --full`".to_string(),
        });
    }
    Ok(SchemaStatus {
        state: SchemaState::Compatible,
        current_version,
        latest_version: LATEST_SCHEMA_VERSION,
        migrations,
        message: "schema is compatible".to_string(),
    })
}

pub fn check_compatible(conn: &Connection) -> anyhow::Result<()> {
    let status = status(conn)?;
    match status.state {
        SchemaState::Compatible => Ok(()),
        SchemaState::Missing => {
            anyhow::bail!(
                "{}",
                "index schema is not initialized; run `rag-rat migrate`, `rag-rat index`, or `rag-rat index --full`"
            )
        },
        SchemaState::Older => anyhow::bail!("{}", status.message),
        SchemaState::Newer => anyhow::bail!("{}", status.message),
        SchemaState::Dirty => anyhow::bail!("{}", status.message),
    }
}

fn apply_baseline(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS index_meta(
            key TEXT PRIMARY KEY,
            value TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS files(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            path TEXT NOT NULL,
            language TEXT NOT NULL,
            kind TEXT NOT NULL,
            sha256 TEXT NOT NULL,
            modified_at_ms INTEGER NOT NULL,
            generated INTEGER NOT NULL DEFAULT 0,
            indexed_at_ms INTEGER NOT NULL,
            indexed_revision TEXT NOT NULL DEFAULT '',
            commit_sha TEXT NOT NULL DEFAULT '',
            worktree_id TEXT NOT NULL DEFAULT '',
            UNIQUE(path, commit_sha, worktree_id)
        );

        CREATE TABLE IF NOT EXISTS chunks(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            file_id INTEGER NOT NULL,
            chunk_kind TEXT NOT NULL,
            symbol_path TEXT,
            start_byte INTEGER NOT NULL,
            end_byte INTEGER NOT NULL,
            start_line INTEGER NOT NULL,
            end_line INTEGER NOT NULL,
            text TEXT NOT NULL,
            text_hash TEXT NOT NULL,
            source_revision TEXT NOT NULL DEFAULT '',
            anchor_version INTEGER NOT NULL DEFAULT 1,
            normalized_hash TEXT NOT NULL DEFAULT '',
            start_boundary_hash TEXT NOT NULL DEFAULT '',
            end_boundary_hash TEXT NOT NULL DEFAULT '',
            start_context_hash TEXT NOT NULL DEFAULT '',
            end_context_hash TEXT NOT NULL DEFAULT '',
            context_radius INTEGER NOT NULL DEFAULT 2,
            embedding_policy TEXT NOT NULL DEFAULT 'Embed',
            embedding_priority INTEGER NOT NULL DEFAULT 1,
            FOREIGN KEY(file_id) REFERENCES files(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS symbols(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            file_id INTEGER NOT NULL,
            language TEXT NOT NULL,
            name TEXT NOT NULL,
            qualified_name TEXT NOT NULL,
            kind TEXT NOT NULL,
            start_byte INTEGER NOT NULL,
            end_byte INTEGER NOT NULL,
            signature TEXT,
            docs TEXT,
            FOREIGN KEY(file_id) REFERENCES files(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS logical_symbols(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            language TEXT NOT NULL,
            path TEXT NOT NULL,
            logical_name TEXT NOT NULL,
            qualified_name TEXT NOT NULL,
            kind TEXT NOT NULL,
            variant_count INTEGER NOT NULL,
            group_reason TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS logical_symbol_members(
            logical_symbol_id INTEGER NOT NULL,
            symbol_id INTEGER NOT NULL,
            cfg_expr TEXT,
            signature_hash TEXT,
            start_line INTEGER NOT NULL,
            end_line INTEGER NOT NULL,
            PRIMARY KEY(logical_symbol_id, symbol_id),
            FOREIGN KEY(logical_symbol_id) REFERENCES logical_symbols(id) ON DELETE CASCADE,
            FOREIGN KEY(symbol_id) REFERENCES symbols(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS symbol_facts(
            symbol_id INTEGER NOT NULL,
            fact_kind TEXT NOT NULL,
            fact_value TEXT NOT NULL,
            PRIMARY KEY(symbol_id, fact_kind, fact_value),
            FOREIGN KEY(symbol_id) REFERENCES symbols(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS edges(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            source_file_id INTEGER,
            from_symbol_id INTEGER,
            to_symbol_id INTEGER,
            from_name TEXT,
            to_name TEXT NOT NULL,
            source_start_line INTEGER NOT NULL DEFAULT 0,
            source_end_line INTEGER NOT NULL DEFAULT 0,
            source_start_byte INTEGER NOT NULL DEFAULT 0,
            source_end_byte INTEGER NOT NULL DEFAULT 0,
            target_start_line INTEGER,
            target_end_line INTEGER,
            target_qualified_name TEXT,
            evidence TEXT,
            receiver_hint TEXT,
            resolution TEXT NOT NULL DEFAULT 'unresolved',
            edge_kind TEXT NOT NULL,
            confidence TEXT NOT NULL,
            FOREIGN KEY(source_file_id) REFERENCES files(id) ON DELETE CASCADE,
            FOREIGN KEY(from_symbol_id) REFERENCES symbols(id) ON DELETE SET NULL,
            FOREIGN KEY(to_symbol_id) REFERENCES symbols(id) ON DELETE SET NULL
        );

        CREATE TABLE IF NOT EXISTS docs(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            chunk_id INTEGER NOT NULL,
            source_kind TEXT NOT NULL,
            heading_path TEXT
        );

        CREATE TABLE IF NOT EXISTS parser_failures(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            path TEXT NOT NULL,
            language TEXT NOT NULL,
            message TEXT NOT NULL
        );

        DROP TABLE IF EXISTS embeddings;
        DROP TABLE IF EXISTS chunk_summaries;

        CREATE TABLE IF NOT EXISTS ai_models(
            model_id TEXT PRIMARY KEY,
            capability TEXT NOT NULL,
            embedding_dim INTEGER,
            runtime TEXT NOT NULL DEFAULT 'local',
            installed INTEGER NOT NULL DEFAULT 0,
            disabled INTEGER NOT NULL DEFAULT 0,
            status TEXT NOT NULL DEFAULT 'MissingModel',
            installed_at_ms INTEGER,
            last_error TEXT
        );

        CREATE TABLE IF NOT EXISTS chunk_embeddings(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            chunk_id INTEGER NOT NULL,
            model_id TEXT NOT NULL,
            model_version TEXT NOT NULL DEFAULT 'v1',
            source_text_hash TEXT NOT NULL,
            input_hash TEXT NOT NULL DEFAULT '',
            embedding_text_version TEXT NOT NULL DEFAULT '',
            embedding_policy TEXT NOT NULL DEFAULT 'Embed',
            embedding_priority INTEGER NOT NULL DEFAULT 1,
            input_chars INTEGER NOT NULL DEFAULT 0,
            input_truncated INTEGER NOT NULL DEFAULT 0,
            embedding_dim INTEGER NOT NULL DEFAULT 0,
            vector_blob BLOB NOT NULL,
            status TEXT NOT NULL,
            attempt_count INTEGER NOT NULL DEFAULT 0,
            last_error_class TEXT,
            next_retry_after_ms INTEGER,
            computed_at_ms INTEGER,
            created_at_ms INTEGER NOT NULL,
            last_error TEXT,
            UNIQUE(chunk_id, model_id),
            FOREIGN KEY(chunk_id) REFERENCES chunks(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS chunk_summaries(
            chunk_id INTEGER NOT NULL,
            model_id TEXT NOT NULL,
            prompt_version TEXT NOT NULL,
            input_hash TEXT NOT NULL,
            text_hash TEXT NOT NULL,
            summary TEXT NOT NULL,
            status TEXT NOT NULL,
            attempt_count INTEGER NOT NULL DEFAULT 0,
            last_error_class TEXT,
            next_retry_after_ms INTEGER,
            computed_at_ms INTEGER,
            PRIMARY KEY(chunk_id, model_id, prompt_version),
            FOREIGN KEY(chunk_id) REFERENCES chunks(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS reconcile_meta(
            key TEXT PRIMARY KEY,
            value TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS reconcile_attempts(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            started_at_ms INTEGER NOT NULL,
            finished_at_ms INTEGER,
            limit_count INTEGER,
            processed_chunks INTEGER NOT NULL DEFAULT 0,
            embeddings_written INTEGER NOT NULL DEFAULT 0,
            blocked_chunks INTEGER NOT NULL DEFAULT 0,
            elapsed_ms INTEGER NOT NULL DEFAULT 0,
            input_chars INTEGER NOT NULL DEFAULT 0,
            batch_size INTEGER NOT NULL DEFAULT 0,
            status TEXT NOT NULL,
            message TEXT
        );

        CREATE TABLE IF NOT EXISTS git_commits(
            hash TEXT PRIMARY KEY,
            author_name TEXT NOT NULL,
            author_email TEXT NOT NULL,
            authored_at_s INTEGER NOT NULL,
            committed_at_s INTEGER NOT NULL,
            subject TEXT NOT NULL,
            body TEXT NOT NULL,
            changed_file_count INTEGER NOT NULL DEFAULT 0
        );

        CREATE TABLE IF NOT EXISTS git_file_changes(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            commit_hash TEXT NOT NULL,
            path TEXT NOT NULL,
            additions INTEGER,
            deletions INTEGER,
            change_kind TEXT NOT NULL DEFAULT 'modified',
            FOREIGN KEY(commit_hash) REFERENCES git_commits(hash) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS git_chunk_blame(
            chunk_id INTEGER PRIMARY KEY,
            source_text_hash TEXT NOT NULL,
            path TEXT NOT NULL,
            start_line INTEGER NOT NULL,
            end_line INTEGER NOT NULL,
            line_count INTEGER NOT NULL,
            dominant_commit TEXT,
            dominant_commit_lines INTEGER NOT NULL DEFAULT 0,
            newest_commit TEXT,
            newest_commit_time_s INTEGER,
            oldest_commit TEXT,
            oldest_commit_time_s INTEGER,
            commit_counts_json TEXT NOT NULL,
            computed_at_ms INTEGER NOT NULL,
            FOREIGN KEY(chunk_id) REFERENCES chunks(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS github_refs(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            ref_kind TEXT NOT NULL DEFAULT 'unknown',
            source_kind TEXT NOT NULL,
            source_path TEXT,
            source_commit TEXT,
            source_text TEXT NOT NULL,
            discovered_at_ms INTEGER NOT NULL
        );

        CREATE TABLE IF NOT EXISTS github_issues(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            html_url TEXT NOT NULL,
            state TEXT NOT NULL,
            title TEXT NOT NULL,
            body TEXT NOT NULL,
            author TEXT,
            created_at TEXT,
            updated_at TEXT,
            is_pull_request INTEGER NOT NULL DEFAULT 0,
            synced_at_ms INTEGER NOT NULL,
            UNIQUE(owner, repo, number)
        );

        CREATE TABLE IF NOT EXISTS github_comments(
            id INTEGER PRIMARY KEY,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            html_url TEXT NOT NULL,
            body TEXT NOT NULL,
            author TEXT,
            created_at TEXT,
            updated_at TEXT,
            synced_at_ms INTEGER NOT NULL
        );

        CREATE TABLE IF NOT EXISTS github_pull_requests(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            html_url TEXT NOT NULL,
            state TEXT NOT NULL,
            title TEXT NOT NULL,
            body TEXT NOT NULL,
            author TEXT,
            created_at TEXT,
            updated_at TEXT,
            merged_at TEXT,
            synced_at_ms INTEGER NOT NULL,
            UNIQUE(owner, repo, number)
        );

        CREATE TABLE IF NOT EXISTS github_reviews(
            id INTEGER PRIMARY KEY,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            html_url TEXT,
            state TEXT NOT NULL,
            body TEXT NOT NULL,
            author TEXT,
            submitted_at TEXT,
            synced_at_ms INTEGER NOT NULL
        );

        CREATE TABLE IF NOT EXISTS github_review_comments(
            id INTEGER PRIMARY KEY,
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            path TEXT,
            html_url TEXT NOT NULL,
            body TEXT NOT NULL,
            author TEXT,
            created_at TEXT,
            updated_at TEXT,
            synced_at_ms INTEGER NOT NULL
        );

        CREATE TABLE IF NOT EXISTS github_ref_sync(
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            status TEXT NOT NULL,
            synced_at_ms INTEGER NOT NULL,
            last_error TEXT,
            PRIMARY KEY(owner, repo, number)
        );

        CREATE TABLE IF NOT EXISTS repo_memories(
            id TEXT PRIMARY KEY,
            kind TEXT NOT NULL,
            title TEXT NOT NULL,
            body TEXT NOT NULL,
            confidence TEXT NOT NULL,
            status TEXT NOT NULL,
            created_by TEXT,
            created_at_ms INTEGER NOT NULL,
            updated_at_ms INTEGER NOT NULL,
            source TEXT NOT NULL,
            source_text_hash TEXT,
            input_hash TEXT,
            memory_version TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS repo_memory_bindings(
            memory_id TEXT NOT NULL,
            binding_kind TEXT NOT NULL,
            binding_id TEXT NOT NULL,
            path TEXT,
            start_line INTEGER,
            end_line INTEGER,
            logical_symbol_id INTEGER,
            symbol_id INTEGER,
            chunk_id INTEGER,
            edge_id INTEGER,
            commit_hash TEXT,
            github_owner TEXT,
            github_repo TEXT,
            github_number INTEGER,
            anchor_status TEXT NOT NULL,
            created_at_ms INTEGER NOT NULL,
            PRIMARY KEY(memory_id, binding_kind, binding_id),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS repo_memory_tags(
            memory_id TEXT NOT NULL,
            tag TEXT NOT NULL,
            PRIMARY KEY(memory_id, tag),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS repo_memory_call_paths(
            memory_id TEXT NOT NULL,
            start_logical_symbol_id INTEGER,
            end_logical_symbol_id INTEGER,
            edge_sequence_hash TEXT NOT NULL,
            path_summary TEXT NOT NULL,
            created_at_ms INTEGER NOT NULL,
            PRIMARY KEY(memory_id, edge_sequence_hash),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE VIRTUAL TABLE IF NOT EXISTS chunk_fts USING fts5(
            text,
            content='chunks',
            content_rowid='id',
            tokenize='porter'
        );

        CREATE VIRTUAL TABLE IF NOT EXISTS commit_fts USING fts5(
            subject,
            body,
            content='git_commits',
            content_rowid='rowid',
            tokenize='porter'
        );

        CREATE VIRTUAL TABLE IF NOT EXISTS github_fts USING fts5(
            owner,
            repo,
            number UNINDEXED,
            item_kind UNINDEXED,
            item_id UNINDEXED,
            url UNINDEXED,
            title,
            body,
            classification,
            tokenize='porter'
        );

        CREATE VIRTUAL TABLE IF NOT EXISTS repo_memory_fts USING fts5(
            memory_id UNINDEXED,
            title,
            body,
            kind,
            tags,
            tokenize='porter'
        );

        CREATE INDEX IF NOT EXISTS idx_files_language ON files(language);
        CREATE INDEX IF NOT EXISTS idx_chunks_file ON chunks(file_id);
        CREATE INDEX IF NOT EXISTS idx_symbols_name ON symbols(name);
        CREATE INDEX IF NOT EXISTS idx_symbols_qualified_name ON symbols(qualified_name);
        CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_id);
        CREATE INDEX IF NOT EXISTS idx_symbol_facts_kind_value
            ON symbol_facts(fact_kind, fact_value);
        CREATE INDEX IF NOT EXISTS idx_logical_symbols_qualified_name
            ON logical_symbols(qualified_name);
        CREATE INDEX IF NOT EXISTS idx_logical_symbol_members_symbol
            ON logical_symbol_members(symbol_id);
        CREATE INDEX IF NOT EXISTS idx_edges_from_symbol ON edges(from_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_edges_to_symbol ON edges(to_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_git_file_changes_path ON git_file_changes(path);
        CREATE INDEX IF NOT EXISTS idx_git_file_changes_commit ON git_file_changes(commit_hash);
        CREATE INDEX IF NOT EXISTS idx_github_refs_path ON github_refs(source_path);
        CREATE INDEX IF NOT EXISTS idx_github_refs_issue ON github_refs(owner, repo, number);
        CREATE UNIQUE INDEX IF NOT EXISTS idx_github_refs_unique
            ON github_refs(owner, repo, number, source_kind, COALESCE(source_path, ''), COALESCE(source_commit, ''), source_text);
        CREATE INDEX IF NOT EXISTS idx_github_review_comments_path ON github_review_comments(path);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_logical_symbol
            ON repo_memory_bindings(logical_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_symbol
            ON repo_memory_bindings(symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_chunk
            ON repo_memory_bindings(chunk_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_edge
            ON repo_memory_bindings(edge_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_path
            ON repo_memory_bindings(path);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_start
            ON repo_memory_call_paths(start_logical_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_end
            ON repo_memory_call_paths(end_logical_symbol_id);
        ",
    )?;
    migrate_files(conn)?;
    migrate_chunks(conn)?;
    migrate_edges(conn)?;
    conn.execute_batch(
        "
        CREATE INDEX IF NOT EXISTS idx_edges_from_name ON edges(from_name);
        CREATE INDEX IF NOT EXISTS idx_edges_to_name ON edges(to_name);
        ",
    )?;
    apply_embedding_vector_metadata(conn)?;
    apply_derived_artifact_reconcile_metadata(conn)?;
    apply_edge_source_target_spans(conn)?;
    apply_embedding_policy_and_input_hash(conn)?;
    apply_logical_symbol_groups(conn)?;
    apply_github_ref_sync(conn)?;
    apply_symbol_facts(conn)?;
    apply_repo_memories(conn)?;
    apply_repo_memory_call_paths(conn)?;
    apply_graph_file_lookup_indexes(conn)?;
    Ok(())
}

pub fn rebuild_fts(conn: &Connection) -> anyhow::Result<()> {
    conn.execute_batch(
        "
        DELETE FROM chunk_fts;
        INSERT INTO chunk_fts(rowid, text)
        SELECT id, text FROM chunks;
        DELETE FROM commit_fts;
        INSERT INTO commit_fts(rowid, subject, body)
        SELECT rowid, subject, body FROM git_commits;
        ",
    )?;
    Ok(())
}

fn migrate_files(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "files", "indexed_revision", "TEXT NOT NULL DEFAULT ''")?;
    conn.execute("UPDATE files SET indexed_revision = sha256 WHERE indexed_revision = ''", [])?;
    Ok(())
}

fn migrate_chunks(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "chunks", "source_revision", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "anchor_version", "INTEGER NOT NULL DEFAULT 1")?;
    add_column_if_missing(conn, "chunks", "normalized_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "start_boundary_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "end_boundary_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "start_context_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "end_context_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "chunks", "context_radius", "INTEGER NOT NULL DEFAULT 2")?;
    add_column_if_missing(conn, "chunks", "embedding_policy", "TEXT NOT NULL DEFAULT 'Embed'")?;
    add_column_if_missing(conn, "chunks", "embedding_priority", "INTEGER NOT NULL DEFAULT 1")?;
    conn.execute(
        "
        UPDATE chunks
        SET source_revision = (
            SELECT files.indexed_revision
            FROM files
            WHERE files.id = chunks.file_id
        )
        WHERE source_revision = ''
        ",
        [],
    )?;
    Ok(())
}

fn migrate_edges(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "edges", "source_file_id", "INTEGER")?;
    add_column_if_missing(conn, "edges", "from_name", "TEXT")?;
    add_column_if_missing(conn, "edges", "to_name", "TEXT NOT NULL DEFAULT ''")?;
    apply_edge_source_target_spans(conn)?;
    apply_edge_evidence_and_resolution(conn)?;
    conn.execute(
        "
        UPDATE edges
        SET from_name = COALESCE(from_name, (
                SELECT qualified_name FROM symbols WHERE symbols.id = edges.from_symbol_id
            )),
            to_name = CASE
                WHEN to_name != '' THEN to_name
                ELSE COALESCE((SELECT qualified_name FROM symbols WHERE symbols.id = edges.to_symbol_id), '')
            END
        ",
        [],
    )?;
    conn.execute("DELETE FROM edges WHERE to_name = ''", [])?;
    conn.execute(
        "
        UPDATE edges
        SET confidence = 'NameOnly'
        WHERE confidence NOT IN ('Exact', 'Syntactic', 'NameOnly', 'Ambiguous')
        ",
        [],
    )?;
    Ok(())
}

fn apply_edge_source_target_spans(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "edges", "source_start_line", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "edges", "source_end_line", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "edges", "source_start_byte", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "edges", "source_end_byte", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "edges", "target_start_line", "INTEGER")?;
    add_column_if_missing(conn, "edges", "target_end_line", "INTEGER")?;
    Ok(())
}

fn apply_edge_evidence_and_resolution(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "edges", "target_qualified_name", "TEXT")?;
    add_column_if_missing(conn, "edges", "evidence", "TEXT")?;
    add_column_if_missing(conn, "edges", "receiver_hint", "TEXT")?;
    add_column_if_missing(conn, "edges", "resolution", "TEXT NOT NULL DEFAULT 'unresolved'")?;
    conn.execute(
        "
        UPDATE edges
        SET resolution = CASE
            WHEN to_symbol_id IS NOT NULL AND confidence = 'Exact' THEN 'exact'
            WHEN to_symbol_id IS NOT NULL AND confidence = 'Syntactic' THEN 'syntactic'
            WHEN to_symbol_id IS NOT NULL AND confidence = 'Ambiguous' THEN 'ambiguous'
            WHEN to_symbol_id IS NOT NULL THEN 'name_fallback'
            ELSE COALESCE(NULLIF(resolution, ''), 'unresolved')
        END
        ",
        [],
    )?;
    Ok(())
}

fn apply_embedding_vector_metadata(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "ai_models", "embedding_dim", "INTEGER")?;
    add_column_if_missing(conn, "ai_models", "runtime", "TEXT NOT NULL DEFAULT 'local'")?;
    add_column_if_missing(conn, "chunk_embeddings", "embedding_dim", "INTEGER NOT NULL DEFAULT 0")?;
    conn.execute(
        "
        UPDATE ai_models
        SET embedding_dim = CASE
                WHEN capability = 'embedding' THEN COALESCE(embedding_dim, 384)
                ELSE embedding_dim
            END,
            runtime = COALESCE(runtime, 'local')
        ",
        [],
    )?;
    Ok(())
}

fn apply_derived_artifact_reconcile_metadata(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "chunk_embeddings", "model_version", "TEXT NOT NULL DEFAULT 'v1'")?;
    add_column_if_missing(conn, "chunk_embeddings", "attempt_count", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "chunk_embeddings", "last_error_class", "TEXT")?;
    add_column_if_missing(conn, "chunk_embeddings", "next_retry_after_ms", "INTEGER")?;
    add_column_if_missing(conn, "chunk_embeddings", "computed_at_ms", "INTEGER")?;
    conn.execute(
        "
        UPDATE chunk_embeddings
        SET model_version = CASE
                WHEN model_id = 'embedding-hash' AND model_version = 'v1' THEN 'hash-v1'
                WHEN model_id = 'fastembed-all-minilm-l6-v2' AND model_version = 'v1'
                    THEN 'fastembed-all-minilm-l6-v2-v1'
                ELSE model_version
            END,
            computed_at_ms = COALESCE(computed_at_ms, created_at_ms),
            attempt_count = CASE
                WHEN attempt_count = 0 AND status IN ('Current', 'Failed', 'Blocked') THEN 1
                ELSE attempt_count
            END,
            last_error_class = CASE
                WHEN last_error IS NOT NULL AND last_error_class IS NULL THEN status
                ELSE last_error_class
            END
        ",
        [],
    )?;
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS chunk_summaries(
            chunk_id INTEGER NOT NULL,
            model_id TEXT NOT NULL,
            prompt_version TEXT NOT NULL,
            input_hash TEXT NOT NULL,
            text_hash TEXT NOT NULL,
            summary TEXT NOT NULL,
            status TEXT NOT NULL,
            attempt_count INTEGER NOT NULL DEFAULT 0,
            last_error_class TEXT,
            next_retry_after_ms INTEGER,
            computed_at_ms INTEGER,
            PRIMARY KEY(chunk_id, model_id, prompt_version),
            FOREIGN KEY(chunk_id) REFERENCES chunks(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS reconcile_meta(
            key TEXT PRIMARY KEY,
            value TEXT NOT NULL
        );
        ",
    )?;
    Ok(())
}

fn apply_embedding_policy_and_input_hash(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "chunks", "embedding_policy", "TEXT NOT NULL DEFAULT 'Embed'")?;
    add_column_if_missing(conn, "chunks", "embedding_priority", "INTEGER NOT NULL DEFAULT 1")?;
    add_column_if_missing(conn, "chunk_embeddings", "input_hash", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(
        conn,
        "chunk_embeddings",
        "embedding_text_version",
        "TEXT NOT NULL DEFAULT ''",
    )?;
    add_column_if_missing(
        conn,
        "chunk_embeddings",
        "embedding_policy",
        "TEXT NOT NULL DEFAULT 'Embed'",
    )?;
    add_column_if_missing(
        conn,
        "chunk_embeddings",
        "embedding_priority",
        "INTEGER NOT NULL DEFAULT 1",
    )?;
    add_column_if_missing(conn, "chunk_embeddings", "input_chars", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(
        conn,
        "chunk_embeddings",
        "input_truncated",
        "INTEGER NOT NULL DEFAULT 0",
    )?;
    add_column_if_missing(conn, "reconcile_attempts", "elapsed_ms", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "reconcile_attempts", "input_chars", "INTEGER NOT NULL DEFAULT 0")?;
    add_column_if_missing(conn, "reconcile_attempts", "batch_size", "INTEGER NOT NULL DEFAULT 0")?;
    Ok(())
}

fn apply_github_ref_sync(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS github_ref_sync(
            owner TEXT NOT NULL,
            repo TEXT NOT NULL,
            number INTEGER NOT NULL,
            status TEXT NOT NULL,
            synced_at_ms INTEGER NOT NULL,
            last_error TEXT,
            PRIMARY KEY(owner, repo, number)
        );
        ",
    )?;
    Ok(())
}

fn apply_symbol_facts(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS symbol_facts(
            symbol_id INTEGER NOT NULL,
            fact_kind TEXT NOT NULL,
            fact_value TEXT NOT NULL,
            PRIMARY KEY(symbol_id, fact_kind, fact_value),
            FOREIGN KEY(symbol_id) REFERENCES symbols(id) ON DELETE CASCADE
        );

        CREATE INDEX IF NOT EXISTS idx_symbol_facts_kind_value
            ON symbol_facts(fact_kind, fact_value);
        ",
    )?;
    Ok(())
}

fn apply_repo_memories(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS repo_memories(
            id TEXT PRIMARY KEY,
            kind TEXT NOT NULL,
            title TEXT NOT NULL,
            body TEXT NOT NULL,
            confidence TEXT NOT NULL,
            status TEXT NOT NULL,
            created_by TEXT,
            created_at_ms INTEGER NOT NULL,
            updated_at_ms INTEGER NOT NULL,
            source TEXT NOT NULL,
            source_text_hash TEXT,
            input_hash TEXT,
            memory_version TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS repo_memory_bindings(
            memory_id TEXT NOT NULL,
            binding_kind TEXT NOT NULL,
            binding_id TEXT NOT NULL,
            path TEXT,
            start_line INTEGER,
            end_line INTEGER,
            logical_symbol_id INTEGER,
            symbol_id INTEGER,
            chunk_id INTEGER,
            edge_id INTEGER,
            commit_hash TEXT,
            github_owner TEXT,
            github_repo TEXT,
            github_number INTEGER,
            anchor_status TEXT NOT NULL,
            created_at_ms INTEGER NOT NULL,
            PRIMARY KEY(memory_id, binding_kind, binding_id),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS repo_memory_tags(
            memory_id TEXT NOT NULL,
            tag TEXT NOT NULL,
            PRIMARY KEY(memory_id, tag),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE TABLE IF NOT EXISTS repo_memory_call_paths(
            memory_id TEXT NOT NULL,
            start_logical_symbol_id INTEGER,
            end_logical_symbol_id INTEGER,
            edge_sequence_hash TEXT NOT NULL,
            path_summary TEXT NOT NULL,
            created_at_ms INTEGER NOT NULL,
            PRIMARY KEY(memory_id, edge_sequence_hash),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE VIRTUAL TABLE IF NOT EXISTS repo_memory_fts USING fts5(
            memory_id UNINDEXED,
            title,
            body,
            kind,
            tags,
            tokenize='porter'
        );

        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_logical_symbol
            ON repo_memory_bindings(logical_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_symbol
            ON repo_memory_bindings(symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_chunk
            ON repo_memory_bindings(chunk_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_edge
            ON repo_memory_bindings(edge_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_path
            ON repo_memory_bindings(path);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_start
            ON repo_memory_call_paths(start_logical_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_end
            ON repo_memory_call_paths(end_logical_symbol_id);
        ",
    )?;
    Ok(())
}

fn apply_repo_memory_call_paths(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS repo_memory_call_paths(
            memory_id TEXT NOT NULL,
            start_logical_symbol_id INTEGER,
            end_logical_symbol_id INTEGER,
            edge_sequence_hash TEXT NOT NULL,
            path_summary TEXT NOT NULL,
            created_at_ms INTEGER NOT NULL,
            PRIMARY KEY(memory_id, edge_sequence_hash),
            FOREIGN KEY(memory_id) REFERENCES repo_memories(id) ON DELETE CASCADE
        );

        CREATE INDEX IF NOT EXISTS idx_repo_memory_bindings_edge
            ON repo_memory_bindings(edge_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_start
            ON repo_memory_call_paths(start_logical_symbol_id);
        CREATE INDEX IF NOT EXISTS idx_repo_memory_call_paths_end
            ON repo_memory_call_paths(end_logical_symbol_id);
        ",
    )?;
    Ok(())
}

fn apply_graph_file_lookup_indexes(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "edges", "source_file_id", "INTEGER")?;
    conn.execute_batch(
        "
        CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_id);
        CREATE INDEX IF NOT EXISTS idx_edges_source_file ON edges(source_file_id);
        ",
    )?;
    Ok(())
}

fn apply_logical_symbol_groups(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        CREATE TABLE IF NOT EXISTS logical_symbols(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            language TEXT NOT NULL,
            path TEXT NOT NULL,
            logical_name TEXT NOT NULL,
            qualified_name TEXT NOT NULL,
            kind TEXT NOT NULL,
            variant_count INTEGER NOT NULL,
            group_reason TEXT NOT NULL
        );

        CREATE TABLE IF NOT EXISTS logical_symbol_members(
            logical_symbol_id INTEGER NOT NULL,
            symbol_id INTEGER NOT NULL,
            cfg_expr TEXT,
            signature_hash TEXT,
            start_line INTEGER NOT NULL,
            end_line INTEGER NOT NULL,
            PRIMARY KEY(logical_symbol_id, symbol_id),
            FOREIGN KEY(logical_symbol_id) REFERENCES logical_symbols(id) ON DELETE CASCADE,
            FOREIGN KEY(symbol_id) REFERENCES symbols(id) ON DELETE CASCADE
        );

        CREATE INDEX IF NOT EXISTS idx_logical_symbols_qualified_name
            ON logical_symbols(qualified_name);
        CREATE INDEX IF NOT EXISTS idx_logical_symbol_members_symbol
            ON logical_symbol_members(symbol_id);
        ",
    )?;
    Ok(())
}

fn applied_migrations(conn: &Connection) -> anyhow::Result<Vec<AppliedMigration>> {
    let mut stmt = conn.prepare(
        "
        SELECT id, applied_at_ms, checksum, description
        FROM schema_version
        ORDER BY applied_at_ms, id
        ",
    )?;
    let rows = stmt.query_map([], |row| {
        Ok(AppliedMigration {
            id: row.get(0)?,
            applied_at_ms: row.get(1)?,
            checksum: row.get(2)?,
            description: row.get(3)?,
        })
    })?;
    let mut migrations = Vec::new();
    for row in rows {
        migrations.push(row?);
    }
    Ok(migrations)
}

fn known_version(migrations: &[AppliedMigration]) -> u32 {
    migrations
        .iter()
        .filter_map(|migration| match migration.id.as_str() {
            MIGRATION_001_ID => Some(1),
            MIGRATION_002_ID => Some(2),
            MIGRATION_003_ID => Some(3),
            MIGRATION_004_ID => Some(4),
            MIGRATION_005_ID => Some(5),
            MIGRATION_006_ID => Some(6),
            MIGRATION_007_ID => Some(7),
            MIGRATION_008_ID => Some(8),
            MIGRATION_009_ID => Some(9),
            MIGRATION_010_ID => Some(10),
            MIGRATION_011_ID => Some(11),
            MIGRATION_012_ID => Some(12),
            MIGRATION_013_ID => Some(13),
            _ => None,
        })
        .max()
        .unwrap_or(0)
}

fn known_migration(id: &str) -> bool {
    matches!(
        id,
        MIGRATION_001_ID
            | MIGRATION_002_ID
            | MIGRATION_003_ID
            | MIGRATION_004_ID
            | MIGRATION_005_ID
            | MIGRATION_006_ID
            | MIGRATION_007_ID
            | MIGRATION_008_ID
            | MIGRATION_009_ID
            | MIGRATION_010_ID
            | MIGRATION_011_ID
            | MIGRATION_012_ID
            | MIGRATION_013_ID
            | DIRTY_MIGRATION_ID
    )
}

fn migration_checksum_mismatch(migration: &AppliedMigration) -> bool {
    match migration.id.as_str() {
        MIGRATION_001_ID => migration.checksum != MIGRATION_001_CHECKSUM,
        MIGRATION_002_ID => migration.checksum != MIGRATION_002_CHECKSUM,
        MIGRATION_003_ID => migration.checksum != MIGRATION_003_CHECKSUM,
        MIGRATION_004_ID => migration.checksum != MIGRATION_004_CHECKSUM,
        MIGRATION_005_ID => migration.checksum != MIGRATION_005_CHECKSUM,
        MIGRATION_006_ID => migration.checksum != MIGRATION_006_CHECKSUM,
        MIGRATION_007_ID => migration.checksum != MIGRATION_007_CHECKSUM,
        MIGRATION_008_ID => migration.checksum != MIGRATION_008_CHECKSUM,
        MIGRATION_009_ID => migration.checksum != MIGRATION_009_CHECKSUM,
        MIGRATION_010_ID => migration.checksum != MIGRATION_010_CHECKSUM,
        MIGRATION_011_ID => migration.checksum != MIGRATION_011_CHECKSUM,
        MIGRATION_012_ID => migration.checksum != MIGRATION_012_CHECKSUM,
        MIGRATION_013_ID => migration.checksum != MIGRATION_013_CHECKSUM,
        _ => false,
    }
}

fn record_migration(
    conn: &Connection,
    id: &str,
    checksum: &str,
    description: &str,
) -> rusqlite::Result<()> {
    conn.execute(
        "INSERT OR REPLACE INTO schema_version(id, applied_at_ms, checksum, description)
         VALUES (?1, ?2, ?3, ?4)",
        params![id, now_ms(), checksum, description],
    )?;
    Ok(())
}

fn table_exists(conn: &Connection, table: &str) -> anyhow::Result<bool> {
    let exists = conn
        .query_row(
            "SELECT 1 FROM sqlite_master WHERE type IN ('table', 'virtual table') AND name = ?1",
            [table],
            |_| Ok(()),
        )
        .optional()?
        .is_some();
    Ok(exists)
}

fn now_ms() -> i64 {
    std::time::SystemTime::now()
        .duration_since(std::time::UNIX_EPOCH)
        .map(|duration| i64::try_from(duration.as_millis()).unwrap_or(i64::MAX))
        .unwrap_or(0)
}

fn add_column_if_missing(
    conn: &Connection,
    table: &str,
    column: &str,
    definition: &str,
) -> rusqlite::Result<()> {
    let mut stmt = conn.prepare(&format!("PRAGMA table_info({table})"))?;
    let rows = stmt.query_map([], |row| row.get::<_, String>(1))?;
    for row in rows {
        if row? == column {
            return Ok(());
        }
    }

    conn.execute_batch(&format!("ALTER TABLE {table} ADD COLUMN {column} {definition}"))
}

fn apply_commit_addressable_worktrees(conn: &Connection) -> rusqlite::Result<()> {
    add_column_if_missing(conn, "files", "commit_sha", "TEXT NOT NULL DEFAULT ''")?;
    add_column_if_missing(conn, "files", "worktree_id", "TEXT NOT NULL DEFAULT ''")?;
    rebuild_files_table_for_commit_scopes(conn)?;
    conn.execute_batch(
        "
        CREATE INDEX IF NOT EXISTS idx_files_commit_path ON files(commit_sha, path);
        CREATE INDEX IF NOT EXISTS idx_files_worktree_path ON files(worktree_id, path);
        ",
    )?;
    Ok(())
}

fn rebuild_files_table_for_commit_scopes(conn: &Connection) -> rusqlite::Result<()> {
    conn.execute_batch(
        "
        PRAGMA foreign_keys = OFF;

        CREATE TABLE IF NOT EXISTS files_new(
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            path TEXT NOT NULL,
            language TEXT NOT NULL,
            kind TEXT NOT NULL,
            sha256 TEXT NOT NULL,
            modified_at_ms INTEGER NOT NULL,
            generated INTEGER NOT NULL DEFAULT 0,
            indexed_at_ms INTEGER NOT NULL,
            indexed_revision TEXT NOT NULL DEFAULT '',
            commit_sha TEXT NOT NULL DEFAULT '',
            worktree_id TEXT NOT NULL DEFAULT '',
            UNIQUE(path, commit_sha, worktree_id)
        );

        INSERT OR IGNORE INTO files_new(
            id, path, language, kind, sha256, modified_at_ms, generated, indexed_at_ms,
            indexed_revision, commit_sha, worktree_id
        )
        SELECT
            id, path, language, kind, sha256, modified_at_ms, generated, indexed_at_ms,
            indexed_revision, COALESCE(commit_sha, ''), COALESCE(worktree_id, '')
        FROM files;

        DROP TABLE files;
        ALTER TABLE files_new RENAME TO files;

        PRAGMA foreign_keys = ON;
        ",
    )
}