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Add internal-schema versioning + auto-migration for __manifest
The on-disk shape of `__manifest` is reconciled with the binary via a single stamp + dispatcher in `db/manifest/migrations.rs`: - `INTERNAL_MANIFEST_SCHEMA_VERSION = 2` declares the shape this binary writes. - The on-disk stamp `omnigraph:internal_schema_version` lives in the manifest dataset's schema-level metadata (Lance `update_schema_metadata`). - `migrate_internal_schema(&mut dataset)` walks `match`-arm steps forward from the on-disk stamp until it matches the binary, then returns. Idempotent. - `init_manifest_repo` stamps the current version at creation; the publisher's open-for-write path runs pending migrations before reading state. Reads stay side-effect-free. - Forward-version protection: a stamp higher than the binary's known version triggers a clear "upgrade omnigraph first" error so an old binary cannot clobber a newer schema. Self-heals existing pre-MR-766 deployments by auto-applying the v1→v2 step: the `lance-schema:unenforced-primary-key` annotation on `__manifest.object_id` that engages Lance's row-level CAS at commit time. New repos created via `init` are stamped at v2 immediately and don't need migration. Adding a future on-disk shape change is one constant bump, one match arm in `migrate_internal_schema`, and one test — no new branches in unrelated code paths. Code outside the migration module never inspects the stamp. New tests in `manifest/tests.rs`: - `test_init_stamps_internal_schema_version` - `test_publish_migrates_pre_stamp_manifest_to_current_version` - `test_publish_rejects_manifest_stamped_at_future_version` Docs: `docs/storage.md`, `docs/maintenance.md`, `docs/constants.md` updated per the AGENTS.md maintenance contract.
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| Run branch prefix | `__run__` | `db/run_registry.rs` |
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| Schema apply lock | `__schema_apply_lock__` | `db/mod.rs` |
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| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | `db/manifest/publisher.rs` |
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| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 2` | `db/manifest/migrations.rs` |
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| Merge stage batch | `MERGE_STAGE_BATCH_ROWS = 8192` | `exec/merge.rs` |
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| Maintenance concurrency | `OMNIGRAPH_MAINTENANCE_CONCURRENCY=8` | `db/omnigraph/optimize.rs` |
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| Graph index cache size | `8` (LRU) | `runtime_cache.rs` |
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