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
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# Constants & Tunables (cheat sheet)
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| Name | Value | Where |
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|---|---|---|
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| `MANIFEST_DIR` | `__manifest` | `db/manifest/layout.rs` |
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| Commit graph dir | `_graph_commits.lance` | `db/commit_graph.rs` |
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feat(engine): sweep & remove legacy __run__ branch guard (MR-770) (#132)
* feat(engine): sweep legacy __run__ branches via v2→v3 manifest migration
Pre-v0.4.0 graphs can carry stale `__run__<id>` staging branches on the
`__manifest` dataset, left by the Run state machine removed in MR-771. Lance's
`list_branches` still enumerates them, so they leak into `branch_list()` and
count as blocking branches at schema-apply time.
Add a one-time `migrate_v2_to_v3` arm to the internal-schema dispatcher: on the
first read-write open it enumerates `__manifest` branches, deletes every
`__run__*` ref, and bumps the stamp to 3. Idempotent under retry (re-enumerates
fresh each run). The `"__run__"` prefix is inlined so the migration does not
depend on the run_registry guard that MR-770 removes next.
This is the prerequisite sweep; the guard removal follows in the next commit.
* refactor(engine): remove the legacy __run__ branch guard (MR-770)
With the v2→v3 migration sweeping stale `__run__*` branches off `__manifest`
on first read-write open, the defense-in-depth `is_internal_run_branch` guard
is no longer needed.
- delete `db/run_registry.rs`; drop the module + re-export from `db/mod.rs`
- collapse `is_internal_system_branch` to the schema-apply-lock check only
- `ensure_public_branch_ref`: drop the run-ref rejection; `__run__*` is now an
ordinary branch name
- `branch_merge`: reject `is_internal_system_branch` (was run-only) so the
schema-apply lock is rejected consistently with create/delete — a small,
deliberate tightening
- update the inline schema-apply test + the writes integration tests
(`public_branch_apis_reject_internal_run_refs` →
`public_branch_apis_reject_internal_system_refs`, which also asserts
`__run__*` now creates successfully)
- docs: flip the "pending production sweep / defense-in-depth" notes to
"auto-swept by the v2→v3 migration"; document the read-only-open limitation
Known residual: the inert `_graph_runs.lance` / `_graph_run_actors.lance` bytes
remain until a `StorageAdapter::delete_prefix` primitive lands.
* fix(engine): run __run__ sweep at Omnigraph::open, not only on publish
Review (PR #132) caught a regression: removing __run__ from
`is_internal_system_branch` exposed legacy `__run__*` branches to the
schema-apply blocking-branch checks (schema_apply.rs:104 and :778) and to
`branch_list()`, but the v2→v3 sweep ran only inside the publisher's
`load_publish_state`. On a pre-v0.4.0 graph whose first write is a schema
apply, the blocking-branch check fires before any publish, so apply failed
with "found non-main branches: __run__…". The same lazy timing also created a
reverse hazard: a user-created `__run__*` branch on a still-v2 graph could be
deleted by the first publish's sweep.
Fix: run the internal-schema migration in `Omnigraph::open(ReadWrite)` (new
`manifest::migrate_on_open`), before the coordinator reads branch state. The
sweep now lands before any branch-observing code, and a graph is stamped v3 at
open — so the one-time sweep can never catch a legitimately-created branch.
Both checks and `branch_list` see the swept graph; correct by construction for
every write path.
Accepted residual: a read-only open of an unmigrated legacy graph still lists
`__run__*` (read-only opens must not write, so they can't sweep). Documented.
Regression test `legacy_run_branch_is_swept_on_open_and_does_not_block_schema_apply`
confirmed RED before the fix (panicked on the branch_list leak assertion) and
GREEN after. Also updates the stale schema_apply.rs comment, the writes.md
"Migration code" section, and adds the v3 row to storage.md's migration table.
* test(engine): sweep multiple legacy __run__ branches; doc nit
Strengthen the v2→v3 migration test to synthesize three `__run__*` branches
(a real legacy graph accumulates one per run) so the migration's delete loop
is exercised on a single reused dataset handle, not just a single branch.
Confirms multi-branch deletion is safe.
Also drop a stale "active runs" reference from the branch_delete doc line.
* fix(engine): force-delete in __run__ sweep for concurrency safety
`migrate_v2_to_v3` ran `Dataset::delete_branch` (= `branches().delete(.., false)`),
which errors "BranchContents not found" if the branch is already gone. Since the
sweep now runs in `Omnigraph::open(ReadWrite)`, two processes opening the same
legacy v2 graph concurrently would race: one wins each delete, the other's open
fails. The migration only claimed idempotency under *sequential* retry.
Switch to `Dataset::force_delete_branch` (= `delete(.., true)`), Lance's
documented path for cleaning up zombie branches, which tolerates an
already-absent branch. The sweep is now idempotent under concurrent runners and
robust to partial/zombie state. Found in self-review; no behavior change for the
common single-open path.
* docs(release): note MR-770 __run__ cleanup in v0.6.1
* docs(branches): reconcile branch cleanup semantics
2026-06-07 17:33:14 +02:00
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| Run registry dir (legacy, removed MR-771) | `_graph_runs.lance` | inert post-v0.4.0; bytes remain until a `delete_prefix` primitive lands |
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| Run branch prefix (legacy, removed MR-771/MR-770) | `__run__` | swept off `__manifest` by the v2→v3 migration; no longer a reserved name |
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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
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| Schema apply lock | `__schema_apply_lock__` | `db/mod.rs` |
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2026-04-29 07:56:18 +00:00
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| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | `db/manifest/publisher.rs` |
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feat(engine): sweep & remove legacy __run__ branch guard (MR-770) (#132)
* feat(engine): sweep legacy __run__ branches via v2→v3 manifest migration
Pre-v0.4.0 graphs can carry stale `__run__<id>` staging branches on the
`__manifest` dataset, left by the Run state machine removed in MR-771. Lance's
`list_branches` still enumerates them, so they leak into `branch_list()` and
count as blocking branches at schema-apply time.
Add a one-time `migrate_v2_to_v3` arm to the internal-schema dispatcher: on the
first read-write open it enumerates `__manifest` branches, deletes every
`__run__*` ref, and bumps the stamp to 3. Idempotent under retry (re-enumerates
fresh each run). The `"__run__"` prefix is inlined so the migration does not
depend on the run_registry guard that MR-770 removes next.
This is the prerequisite sweep; the guard removal follows in the next commit.
* refactor(engine): remove the legacy __run__ branch guard (MR-770)
With the v2→v3 migration sweeping stale `__run__*` branches off `__manifest`
on first read-write open, the defense-in-depth `is_internal_run_branch` guard
is no longer needed.
- delete `db/run_registry.rs`; drop the module + re-export from `db/mod.rs`
- collapse `is_internal_system_branch` to the schema-apply-lock check only
- `ensure_public_branch_ref`: drop the run-ref rejection; `__run__*` is now an
ordinary branch name
- `branch_merge`: reject `is_internal_system_branch` (was run-only) so the
schema-apply lock is rejected consistently with create/delete — a small,
deliberate tightening
- update the inline schema-apply test + the writes integration tests
(`public_branch_apis_reject_internal_run_refs` →
`public_branch_apis_reject_internal_system_refs`, which also asserts
`__run__*` now creates successfully)
- docs: flip the "pending production sweep / defense-in-depth" notes to
"auto-swept by the v2→v3 migration"; document the read-only-open limitation
Known residual: the inert `_graph_runs.lance` / `_graph_run_actors.lance` bytes
remain until a `StorageAdapter::delete_prefix` primitive lands.
* fix(engine): run __run__ sweep at Omnigraph::open, not only on publish
Review (PR #132) caught a regression: removing __run__ from
`is_internal_system_branch` exposed legacy `__run__*` branches to the
schema-apply blocking-branch checks (schema_apply.rs:104 and :778) and to
`branch_list()`, but the v2→v3 sweep ran only inside the publisher's
`load_publish_state`. On a pre-v0.4.0 graph whose first write is a schema
apply, the blocking-branch check fires before any publish, so apply failed
with "found non-main branches: __run__…". The same lazy timing also created a
reverse hazard: a user-created `__run__*` branch on a still-v2 graph could be
deleted by the first publish's sweep.
Fix: run the internal-schema migration in `Omnigraph::open(ReadWrite)` (new
`manifest::migrate_on_open`), before the coordinator reads branch state. The
sweep now lands before any branch-observing code, and a graph is stamped v3 at
open — so the one-time sweep can never catch a legitimately-created branch.
Both checks and `branch_list` see the swept graph; correct by construction for
every write path.
Accepted residual: a read-only open of an unmigrated legacy graph still lists
`__run__*` (read-only opens must not write, so they can't sweep). Documented.
Regression test `legacy_run_branch_is_swept_on_open_and_does_not_block_schema_apply`
confirmed RED before the fix (panicked on the branch_list leak assertion) and
GREEN after. Also updates the stale schema_apply.rs comment, the writes.md
"Migration code" section, and adds the v3 row to storage.md's migration table.
* test(engine): sweep multiple legacy __run__ branches; doc nit
Strengthen the v2→v3 migration test to synthesize three `__run__*` branches
(a real legacy graph accumulates one per run) so the migration's delete loop
is exercised on a single reused dataset handle, not just a single branch.
Confirms multi-branch deletion is safe.
Also drop a stale "active runs" reference from the branch_delete doc line.
* fix(engine): force-delete in __run__ sweep for concurrency safety
`migrate_v2_to_v3` ran `Dataset::delete_branch` (= `branches().delete(.., false)`),
which errors "BranchContents not found" if the branch is already gone. Since the
sweep now runs in `Omnigraph::open(ReadWrite)`, two processes opening the same
legacy v2 graph concurrently would race: one wins each delete, the other's open
fails. The migration only claimed idempotency under *sequential* retry.
Switch to `Dataset::force_delete_branch` (= `delete(.., true)`), Lance's
documented path for cleaning up zombie branches, which tolerates an
already-absent branch. The sweep is now idempotent under concurrent runners and
robust to partial/zombie state. Found in self-review; no behavior change for the
common single-open path.
* docs(release): note MR-770 __run__ cleanup in v0.6.1
* docs(branches): reconcile branch cleanup semantics
2026-06-07 17:33:14 +02:00
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| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 3` | `db/manifest/migrations.rs` |
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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
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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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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
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| Lance blob compaction support | `LANCE_SUPPORTS_BLOB_COMPACTION = false` | `db/omnigraph/optimize.rs` |
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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
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| Graph index cache size | `8` (LRU) | `runtime_cache.rs` |
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| Default body limit | `1 MB` | `omnigraph-server/lib.rs` |
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| Ingest body limit | `32 MB` | `omnigraph-server/lib.rs` |
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| Engine embed model | `gemini-embedding-2-preview` | `omnigraph/embedding.rs` |
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| Compiler embed model | `text-embedding-3-small` | `omnigraph-compiler/embedding.rs` |
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| Embed timeout | `30 000 ms` | both clients |
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| Embed retries | `4` | both clients |
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| Embed retry backoff | `200 ms` | both clients |
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| LANCE memory pool default | `1 GB` (raised in v0.3.0) | runtime |
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