Refactor AGENTS.md from encyclopedia to map; move spec into docs/
Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).
Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
2026-04-28 23:31:08 +02:00
# Maintenance: Optimize & Cleanup
`db/omnigraph/optimize.rs` .
## `optimize_all_tables(db)` — non-destructive
- Lance `compact_files()` on every node + edge table on `main` .
- Rewrites small fragments into fewer large ones; old fragments remain reachable via older manifests.
- Bounded by `OMNIGRAPH_MAINTENANCE_CONCURRENCY` (default 8).
fix(optimize): skip blob-bearing tables to avoid Lance compaction crash (#138)
* test(optimize): pin Lance blob-column compaction failure as a surface guard
Lance compact_files mis-decodes blob-v2 columns under its forced BlobHandling::AllBinary read ("more fields in the schema than provided column indices"), failing even a pristine uniform-V2_2 multi-fragment blob table; reads use descriptor handling and are unaffected.
Guard 10 reproduces this and is self-retiring: it turns red on the Lance bump that fixes the bug, forcing LANCE_SUPPORTS_BLOB_COMPACTION to flip.
* fix(optimize): skip blob-bearing tables instead of crashing compaction
omnigraph optimize aborted the whole sweep when any node/edge table had a Blob property: Lance compact_files cannot decode blob-v2 columns under AllBinary (the column-index error pinned by the surface guard). Skip blob-bearing tables behind a LANCE_SUPPORTS_BLOB_COMPACTION gate and report them via TableOptimizeStats.skipped / SkipReason (surfaced in the CLI and a tracing::warn) instead of erroring, which also isolates the failure so the other tables still compact.
Reads/writes are unaffected; only fragment/space reclamation on blob tables is deferred until the upstream Lance fix. Adds a maintenance.rs regression test (validated red with the column-index symptom before the fix, green after), a concise v0.6.1 release note, and updates docs (maintenance, cli-reference, AGENTS capability matrix, invariants Known Gaps, lance.md audit, constants).
* refactor(optimize): make TableOptimizeStats and SkipReason non_exhaustive
Both are returned result types, never built by callers, so #[non_exhaustive] makes this the last field/variant addition that can break downstream literal construction and keeps future ones non-breaking (review feedback on the public-field addition). The v0.6.1 Compatibility Notes call out the source-level change.
Also drops the now-stale "RED today / GREEN after the fix lands" narration in the optimize_skips_blob_table_and_reports_skip test (historical regression context now that the fix is in this branch), and folds in the expanded v0.6.1 release note.
* chore(release): bump workspace to v0.6.1
Coherent version bump to accompany the v0.6.1 release note: all five crate manifests + path-dependency constraints, Cargo.lock, the AGENTS.md surveyed-version line, and openapi.json info.version move 0.6.0 -> 0.6.1. Matches the established release pattern (#118 landed the v0.6.0 note + bump together) and resolves the Codex/Devin review flag that a v0.6.1 note without a bump leaves CARGO_PKG_VERSION reporting 0.6.0 and mixed package versions.
2026-06-02 17:12:00 +02:00
- Returns `[TableOptimizeStats { table_key, fragments_removed, fragments_added, committed, skipped }]` .
- **Blob tables are skipped.** A table that declares any `Blob` property is not compacted: it is reported with `skipped: Some(BlobColumnsUnsupportedByLance)` (and logged via `tracing::warn` ) instead of compacted, and the rest of the sweep proceeds normally. The current Lance `compact_files` mis-decodes blob-v2 columns under its forced `BlobHandling::AllBinary` read; **reads and writes are unaffected** — only compaction is. This is gated by `LANCE_SUPPORTS_BLOB_COMPACTION` (`db/omnigraph/optimize.rs` ) and removed when the upstream Lance fix lands (see [docs/dev/lance.md ](../dev/lance.md )). Consequence: fragment count and deleted-row space on blob tables are not reclaimed until then; query results are never affected.
Refactor AGENTS.md from encyclopedia to map; move spec into docs/
Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).
Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
2026-04-28 23:31:08 +02:00
## `cleanup_all_tables(db, options)` — destructive
- Lance `cleanup_old_versions()` per table.
- Removes manifests (and their unique fragments) older than the retention policy.
- `CleanupPolicyOptions { keep_versions: Option<u32>, older_than: Option<Duration> }` — at least one is required.
fix(branch): make branch delete correct under partial failure (#137)
* test(lance): pin force_delete_branch surface guard
Pin the Lance 6.0.1 force_delete_branch behavior the branch-delete
single-authority redesign relies on: plain delete_branch errors on a
missing ref, force_delete_branch removes an existing forked branch, and
the local-store quirk where force_delete on a fully-absent branch still
errors (worked around by the upcoming TableStore::force_delete_branch).
Re-pin the docs/dev/lance.md alignment stanza (9 guards; 4 runtime).
* feat(storage): add force branch-delete to TableStore + CommitGraph
Add TableStore::force_delete_branch and CommitGraph::force_delete_branch
(idempotent: tolerate an already-absent branch via Lance RefNotFound /
NotFound), plus CommitGraph::list_branches for the cleanup reconciler to
diff against the manifest authority. RefConflict (referencing
descendants) is still surfaced. Unused until the branch-delete rewire.
* test(maintenance): red — cleanup reconciles orphaned branch forks
Forge a Lance branch on the Person table that the manifest never
references (a zombie fork from an incomplete prior delete) and assert
cleanup reclaims it while leaving main intact. Fails today: cleanup does
not yet reconcile orphaned forks. Goes green with the next commit.
* fix(maintenance): reconcile orphaned branch forks in cleanup
Add reconcile_orphaned_branches: force_delete_branch every per-table and
commit-graph Lance branch absent from the manifest branch set (the
authority), children-before-parents. Folded into cleanup_all_tables,
runs before version GC. Idempotent and authority-derived; no-ops once
nothing is orphaned, and would harmlessly find nothing if a future Lance
atomic multi-dataset branch op prevented orphans. Adds TableStore::list_branches
and exposes graph_commits_uri(pub crate). Turns the maintenance red test green.
* test(failpoints): red — branch_delete partial failure converges
Add the branch_delete.before_table_cleanup failpoint hook (inert without
the feature) and a regression test: a cleanup-step failure after the
manifest authority flip must leave branch_delete returning Ok, the branch
gone, the orphan stranded, then reclaimed by cleanup, and the name
reusable. Fails today: cleanup_deleted_branch_tables propagates the error
as a hard failure. Goes green with the next commit.
* fix(branch): best-effort fork reclaim after the manifest flip
Make branch_delete treat per-table forks and the commit-graph branch as
derived state reclaimed best-effort with force_delete_branch after the
manifest authority flip. A reclaim failure (transient error, or the
branch_delete.before_table_cleanup failpoint) is logged via tracing::warn
and swallowed: the branch is already gone and the cleanup reconciler
converges the orphan. cleanup_deleted_branch_tables no longer returns an
error or blocks the call. Turns the partial-failure recovery test green.
* test(failpoints): red — recreate over orphaned fork is actionable
After a partial-failure delete leaves a fork orphaned, recreating the
branch name and writing to the previously-forked table before cleanup
runs currently surfaces the opaque ExpectedVersionMismatch ("stale view
... expected manifest table version N"). Assert instead a clear error
pointing the user at cleanup. Goes green with the next commit.
* fix(branch): actionable orphan-collision error in fork_branch_from_state
When a fork's create_branch collides with an existing target ref, reuse
it only if its head matches source_version (a legitimate concurrent
first-write). A version mismatch means a zombie fork from an incomplete
prior delete: return a manifest_conflict pointing the user at
`omnigraph cleanup`, instead of the opaque ExpectedVersionMismatch.
Turns the recreate-over-orphan red test green.
* docs(invariants): single-authority branch-lifecycle + Lance forward-compat
Record branch delete in the Current Truth Matrix: manifest is the single
authority flipped atomically first, per-table forks + commit-graph branch
are derived state reclaimed best-effort with the cleanup reconciler as
backstop, and reusing a name whose reclaim failed surfaces an actionable
error. Note the reconciler is authority-derived and degrades to a no-op
under a future Lance atomic multi-dataset branch op, the same shape as
invariant 7.
* test(failpoints): red — cleanup isolates a single-table failure
Add the cleanup.table_gc failpoint hook (inert without the feature) and
an error: Option<String> field on TableCleanupStats (mechanical, always
None for now). Regression test: a one-shot version-GC failure for one
table must not abort the whole cleanup — assert cleanup still succeeds,
surfaces the failure per-table in stats, and the independent reconcile
pass still reclaimed an orphan. Fails today: the version-GC collect
aborts on the first table error. Goes green with the next commit.
* fix(maintenance): fault-isolate cleanup per table
Make the cleanup sweep do as much as it can and converge on re-run
instead of aborting wholesale on one table's transient error
(invariant 13). The version-GC loop now records a per-table failure on
its stats row (error: Some) and logs it rather than collecting into a
Result that aborts; reconcile_orphaned_branches isolates per-table and
commit-graph failures into BranchReconcileStats.failures. The CLI reports
any failed tables and tells the user to rerun cleanup. Addresses the
Devin review finding. Turns the single-table-failure test green.
* test(failpoints): red — branch_create heals commit-graph zombie + is atomic
Add the branch_delete.before_commit_graph_reclaim failpoint hook and two
regression tests: (a) recreating a name whose delete left a commit-graph
zombie must succeed (today it dies on Lance's internal Clone error), and
(b) branch_create must roll back the manifest branch when the derived
commit-graph branch fails (today it leaves the manifest branch created
while returning Err). Both fail now; green with the next commit. The
existing branch_create_failpoint_triggers test still passes.
* fix(branch): make branch_create atomic + heal commit-graph zombie
branch_create now flips the manifest authority first, then creates the
derived commit-graph branch in create_commit_graph_branch, force-dropping
any orphaned commit-graph ref left by an incomplete prior delete (the
manifest branch is fresh, so a same-named commit-graph branch is provably
a zombie). If commit-graph creation fails, the manifest branch is rolled
back so the name never half-exists. Addresses the Codex review finding.
Turns the two branch_create red tests green; existing tests unaffected.
* test(failpoints): red — fork collision misclassifies live concurrent fork
Add the fork.before_classify failpoint hook and a concurrency test: when
a concurrent first-write legitimately wins the fork race, the loser must
get a retryable refresh-and-retry, not the misleading run-cleanup orphan
error. Today the version-comparison misclassifies the live fork as an
orphan (the Cursor finding). Goes green with the next commit.
* fix(branch): manifest-arbitrated fork-collision classification
Classify a fork collision by the manifest authority instead of comparing
Lance branch versions. Before forking, open_owned_dataset_for_branch_write
re-reads the live manifest: if the table is already forked on the active
branch, a concurrent first-write won and the loser gets a retryable
refresh-and-retry (not a misleading orphan error). fork_branch_from_state
no longer guesses from versions — a create collision past that check is
an orphan, so it returns the actionable cleanup error. Addresses the
Cursor finding; turns the live-concurrent-fork test green, zombie path
unchanged.
* test(failpoints): close branch-lifecycle test gaps
Three coverage additions for the branch-delete work (behavior already
correct; these lock it in and catch regressions):
- cleanup_isolates_reconcile_failure: inject a force-delete failure into
the reconcile loop (new cleanup.reconcile_fork hook) and assert the
sweep continues + converges on re-run. Directly covers the reconcile
loop the Devin finding was about (previously only version-GC was).
- cleanup_reclaims_orphaned_commit_graph_branch: forge a commit-graph
orphan via the delete reclaim failpoint and assert cleanup's
reconcile_commit_graph_orphans drops it (previously untested).
- fork_collision_with_live_concurrent_fork_is_retryable: replace the
fixed 300ms sleep with a deterministic readiness signal (cfg_callback +
compare_exchange atomics) so the two-writer ordering can't flake.
Full failpoints suite 31/0.
2026-06-01 13:28:38 +02:00
- Returns `[TableCleanupStats { table_key, bytes_removed, old_versions_removed, error }]` .
- **Fault-isolated per table.** A single table's transient failure (version GC or
orphan reclaim) is recorded on that table's stats row (`error: Some(..)` , logged
via `tracing` ) and never aborts the healthy tables — cleanup is the convergence
backstop, so it does as much as it can and converges on re-run. The CLI reports
any failed tables; rerun `cleanup` to retry them.
Refactor AGENTS.md from encyclopedia to map; move spec into docs/
Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).
Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
2026-04-28 23:31:08 +02:00
- CLI guards with `--confirm` ; without it, prints a preview line.
2026-05-05 16:04:48 +02:00
- **Recovery floor:** `--keep < 3` may garbage-collect Lance versions that the open-time recovery sweep needs as a rollback target (the sweep restores to the branch's manifest-pinned table version, which is HEAD-1 in the typical Phase B → Phase C drift case). Default `--keep 10` is safe.
fix(branch): make branch delete correct under partial failure (#137)
* test(lance): pin force_delete_branch surface guard
Pin the Lance 6.0.1 force_delete_branch behavior the branch-delete
single-authority redesign relies on: plain delete_branch errors on a
missing ref, force_delete_branch removes an existing forked branch, and
the local-store quirk where force_delete on a fully-absent branch still
errors (worked around by the upcoming TableStore::force_delete_branch).
Re-pin the docs/dev/lance.md alignment stanza (9 guards; 4 runtime).
* feat(storage): add force branch-delete to TableStore + CommitGraph
Add TableStore::force_delete_branch and CommitGraph::force_delete_branch
(idempotent: tolerate an already-absent branch via Lance RefNotFound /
NotFound), plus CommitGraph::list_branches for the cleanup reconciler to
diff against the manifest authority. RefConflict (referencing
descendants) is still surfaced. Unused until the branch-delete rewire.
* test(maintenance): red — cleanup reconciles orphaned branch forks
Forge a Lance branch on the Person table that the manifest never
references (a zombie fork from an incomplete prior delete) and assert
cleanup reclaims it while leaving main intact. Fails today: cleanup does
not yet reconcile orphaned forks. Goes green with the next commit.
* fix(maintenance): reconcile orphaned branch forks in cleanup
Add reconcile_orphaned_branches: force_delete_branch every per-table and
commit-graph Lance branch absent from the manifest branch set (the
authority), children-before-parents. Folded into cleanup_all_tables,
runs before version GC. Idempotent and authority-derived; no-ops once
nothing is orphaned, and would harmlessly find nothing if a future Lance
atomic multi-dataset branch op prevented orphans. Adds TableStore::list_branches
and exposes graph_commits_uri(pub crate). Turns the maintenance red test green.
* test(failpoints): red — branch_delete partial failure converges
Add the branch_delete.before_table_cleanup failpoint hook (inert without
the feature) and a regression test: a cleanup-step failure after the
manifest authority flip must leave branch_delete returning Ok, the branch
gone, the orphan stranded, then reclaimed by cleanup, and the name
reusable. Fails today: cleanup_deleted_branch_tables propagates the error
as a hard failure. Goes green with the next commit.
* fix(branch): best-effort fork reclaim after the manifest flip
Make branch_delete treat per-table forks and the commit-graph branch as
derived state reclaimed best-effort with force_delete_branch after the
manifest authority flip. A reclaim failure (transient error, or the
branch_delete.before_table_cleanup failpoint) is logged via tracing::warn
and swallowed: the branch is already gone and the cleanup reconciler
converges the orphan. cleanup_deleted_branch_tables no longer returns an
error or blocks the call. Turns the partial-failure recovery test green.
* test(failpoints): red — recreate over orphaned fork is actionable
After a partial-failure delete leaves a fork orphaned, recreating the
branch name and writing to the previously-forked table before cleanup
runs currently surfaces the opaque ExpectedVersionMismatch ("stale view
... expected manifest table version N"). Assert instead a clear error
pointing the user at cleanup. Goes green with the next commit.
* fix(branch): actionable orphan-collision error in fork_branch_from_state
When a fork's create_branch collides with an existing target ref, reuse
it only if its head matches source_version (a legitimate concurrent
first-write). A version mismatch means a zombie fork from an incomplete
prior delete: return a manifest_conflict pointing the user at
`omnigraph cleanup`, instead of the opaque ExpectedVersionMismatch.
Turns the recreate-over-orphan red test green.
* docs(invariants): single-authority branch-lifecycle + Lance forward-compat
Record branch delete in the Current Truth Matrix: manifest is the single
authority flipped atomically first, per-table forks + commit-graph branch
are derived state reclaimed best-effort with the cleanup reconciler as
backstop, and reusing a name whose reclaim failed surfaces an actionable
error. Note the reconciler is authority-derived and degrades to a no-op
under a future Lance atomic multi-dataset branch op, the same shape as
invariant 7.
* test(failpoints): red — cleanup isolates a single-table failure
Add the cleanup.table_gc failpoint hook (inert without the feature) and
an error: Option<String> field on TableCleanupStats (mechanical, always
None for now). Regression test: a one-shot version-GC failure for one
table must not abort the whole cleanup — assert cleanup still succeeds,
surfaces the failure per-table in stats, and the independent reconcile
pass still reclaimed an orphan. Fails today: the version-GC collect
aborts on the first table error. Goes green with the next commit.
* fix(maintenance): fault-isolate cleanup per table
Make the cleanup sweep do as much as it can and converge on re-run
instead of aborting wholesale on one table's transient error
(invariant 13). The version-GC loop now records a per-table failure on
its stats row (error: Some) and logs it rather than collecting into a
Result that aborts; reconcile_orphaned_branches isolates per-table and
commit-graph failures into BranchReconcileStats.failures. The CLI reports
any failed tables and tells the user to rerun cleanup. Addresses the
Devin review finding. Turns the single-table-failure test green.
* test(failpoints): red — branch_create heals commit-graph zombie + is atomic
Add the branch_delete.before_commit_graph_reclaim failpoint hook and two
regression tests: (a) recreating a name whose delete left a commit-graph
zombie must succeed (today it dies on Lance's internal Clone error), and
(b) branch_create must roll back the manifest branch when the derived
commit-graph branch fails (today it leaves the manifest branch created
while returning Err). Both fail now; green with the next commit. The
existing branch_create_failpoint_triggers test still passes.
* fix(branch): make branch_create atomic + heal commit-graph zombie
branch_create now flips the manifest authority first, then creates the
derived commit-graph branch in create_commit_graph_branch, force-dropping
any orphaned commit-graph ref left by an incomplete prior delete (the
manifest branch is fresh, so a same-named commit-graph branch is provably
a zombie). If commit-graph creation fails, the manifest branch is rolled
back so the name never half-exists. Addresses the Codex review finding.
Turns the two branch_create red tests green; existing tests unaffected.
* test(failpoints): red — fork collision misclassifies live concurrent fork
Add the fork.before_classify failpoint hook and a concurrency test: when
a concurrent first-write legitimately wins the fork race, the loser must
get a retryable refresh-and-retry, not the misleading run-cleanup orphan
error. Today the version-comparison misclassifies the live fork as an
orphan (the Cursor finding). Goes green with the next commit.
* fix(branch): manifest-arbitrated fork-collision classification
Classify a fork collision by the manifest authority instead of comparing
Lance branch versions. Before forking, open_owned_dataset_for_branch_write
re-reads the live manifest: if the table is already forked on the active
branch, a concurrent first-write won and the loser gets a retryable
refresh-and-retry (not a misleading orphan error). fork_branch_from_state
no longer guesses from versions — a create collision past that check is
an orphan, so it returns the actionable cleanup error. Addresses the
Cursor finding; turns the live-concurrent-fork test green, zombie path
unchanged.
* test(failpoints): close branch-lifecycle test gaps
Three coverage additions for the branch-delete work (behavior already
correct; these lock it in and catch regressions):
- cleanup_isolates_reconcile_failure: inject a force-delete failure into
the reconcile loop (new cleanup.reconcile_fork hook) and assert the
sweep continues + converges on re-run. Directly covers the reconcile
loop the Devin finding was about (previously only version-GC was).
- cleanup_reclaims_orphaned_commit_graph_branch: forge a commit-graph
orphan via the delete reclaim failpoint and assert cleanup's
reconcile_commit_graph_orphans drops it (previously untested).
- fork_collision_with_live_concurrent_fork_is_retryable: replace the
fixed 300ms sleep with a deterministic readiness signal (cfg_callback +
compare_exchange atomics) so the two-writer ordering can't flake.
Full failpoints suite 31/0.
2026-06-01 13:28:38 +02:00
- **Orphaned-branch reconciliation:** before the version GC, cleanup runs `reconcile_orphaned_branches` , which `force_delete_branch` es any per-table or commit-graph Lance branch absent from the manifest branch list. These orphans arise when a `branch_delete` flips the manifest authority but a downstream best-effort reclaim does not complete (see [branches-commits.md ](branches-commits.md )). The reconciler is authority-derived and idempotent (it no-ops once nothing is orphaned), runs regardless of the `keep_versions` / `older_than` values (those gate version GC only), and never reclaims `main` or system-branch forks. Reclaimed forks are logged via `tracing::info` .
Refactor AGENTS.md from encyclopedia to map; move spec into docs/
Splits the 990-line AGENTS.md into a 184-line map (architecture,
where-to-find index, always-on invariants, capability matrix,
maintenance contract) plus 18 new docs/*.md files holding the deep
content per topic (storage, schema and query languages, indexes,
embeddings, branches/commits, runs, merge, changes, execution, policy,
server, CLI reference, audit, errors, CI, constants, v0.3.1 notes).
Adds scripts/check-agents-md.sh and a check_agents_md CI job that
verifies every docs/ link in AGENTS.md resolves and every doc in the
canonical set is linked. CLAUDE.md remains a symlink to AGENTS.md.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
2026-04-28 23:31:08 +02:00
## Tombstones
Logical sub-table delete markers in `__manifest` ; `tombstone_object_id(table_key, version)` excludes a sub-table version from snapshot reconstruction.
2026-04-29 11:44:14 +00:00
## Internal schema migrations (`db/manifest/migrations.rs`)
Version evolutions of the on-disk `__manifest` shape are reconciled automatically on the first write under a new binary. `INTERNAL_MANIFEST_SCHEMA_VERSION` declares the shape the binary expects; the on-disk stamp `omnigraph:internal_schema_version` (Lance schema-level metadata) records the on-disk shape. The publisher's open-for-write path calls `migrate_internal_schema` before reading state; reads are side-effect-free. No operator action is required for in-place upgrades. See [storage.md → Internal schema versioning ](storage.md ) for the full mechanism.
A binary opening a manifest stamped at a version *higher* than it knows about refuses to publish with a clear "upgrade omnigraph first" error — old binaries cannot clobber a newer schema.
