* 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
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Branches, Commits, Snapshots
L1 — Lance per-dataset branches
Lance supports branching at the dataset level: a branch is a named lineage of versions, and fork_branch_from_state(source_branch, target_branch, source_version) creates a copy-on-write fork.
L2 — Graph-level branches
OmniGraph builds graph branches on top by branching every sub-table coherently:
branch_create(name)/branch_create_from(target, name)— disallowed namemain; fails if branch exists; ensures the schema-apply lock is idle. Atomic and authority-first likebranch_delete: it flips the__manifestbranch (authority), then creates the derived 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.branch_list()— returns public branches, filters the internal__schema_apply_lock__branch.branch_delete(name)— refuses if there are descendants on the branch, or if it is the current branch. The manifest is the single authority for branch existence: deletion flips the__manifestbranch ref first (one atomic op), after which the branch is gone from every snapshot. The owned per-table forks and the commit-graph branch are derived state, reclaimed best-effort withforce_delete_branchafter the flip. A failure during that reclaim (transient object-store error) does not fail the call or block the authority flip; the leftover forks are unreachable orphans that thecleanupreconciler converges. One consequence: if a delete's best-effort reclaim fails, reusing that branch name before the nextcleanupsurfaces a clear error pointing atcleanup(the stale fork would otherwise collide on first write).- Lazy forking: a branch only forks a sub-table when that sub-table is first mutated on it. Pure-read branches share fragments with their source. A fork collision is classified by the manifest authority, not by Lance branch versions: if the live manifest already records the fork on the active branch, a concurrent first-write won and the caller gets a retryable "refresh and retry"; if the manifest does not, a physical branch there is an orphan and the caller is pointed at
cleanup. sync_branch(branch)— re-binds the in-memory handle to the latest head of the branch.
L2 — Commit graph (db/commit_graph.rs)
In-memory shape of a graph commit:
GraphCommit {
graph_commit_id: ULID,
manifest_branch: Option<String>,
manifest_version: u64,
parent_commit_id: Option<String>,
merged_parent_commit_id: Option<String>, // populated for merge commits
actor_id: Option<String>, // joined in-memory from _graph_commit_actors.lance, NOT a column on _graph_commits.lance
created_at: i64 (microseconds since epoch),
}
Storage is split across two Lance datasets (both with stable row IDs):
_graph_commits.lance— every column above exceptactor_id._graph_commit_actors.lance— optional separate(graph_commit_id, actor_id)map, created on demand. Theactor_idfield above is populated by joining this dataset in-memory at load time.
Notes:
- Every successful publish (load / change / merge / schema_apply) appends one commit.
- Merge commits have two parents; linear commits have one.
- API:
list_commits(branch),get_commit(id),head_commit_id_for_branch(branch).
L2 — Snapshots & time travel
snapshot()— current snapshot for the bound branch; cached.snapshot_of(target)— snapshot at aReadTarget(branch | snapshot id).snapshot_at_version(v: u64)— historical snapshot from any manifest version.entity_at(table_key, id, version)— single-entity time travel without building a full snapshot.- A
Snapshotis a(version, HashMap<table_key, SubTableEntry>)— cheap to build, snapshot-isolated cross-table reads.
L2 — Internal system branches
Internal or legacy branch refs:
__schema_apply_lock__— serializes schema migrations; filtered frombranch_list()but visible to internals.__run__<run-id>— legacy from the pre-v0.4.0 Run state machine (removed in MR-771). These are swept off__manifeston the first read-write open by the v2→v3 internal-schema migration (MR-770), and__run__*is no longer a reserved name. Known limitation: a pre-v0.4.0 graph opened read-only still surfaces any stale__run__*branch inbranch_list()until its first read-write open (the migration is write-path-only, like all manifest migrations).
L2 — Recovery audit trail
The four migrated writers (MutationStaging::finalize, schema_apply, branch_merge, ensure_indices) protect their multi-table commits with a sidecar at __recovery/{ulid}.json written before Phase B and deleted after Phase C. The next Omnigraph::open (gated on OpenMode::ReadWrite) runs the recovery sweep in crates/omnigraph/src/db/manifest/recovery.rs: classify per-table state, decide all-or-nothing per sidecar, roll forward / back, record an audit row.
Audit rows live in _graph_commit_recoveries.lance (sibling to _graph_commits.lance) and reference the commit graph by graph_commit_id. The linked recovery commit is identified by that same graph_commit_id, and actor_id="omnigraph:recovery" is stored in _graph_commit_actors.lance (joined by graph_commit_id) — _graph_commits.lance itself does not carry the actor_id column. To find recoveries for a specific original actor: omnigraph commit list --filter actor=omnigraph:recovery, then join to _graph_commit_recoveries.lance by graph_commit_id to read recovery_for_actor. Schema: see crates/omnigraph/src/db/recovery_audit.rs.