Content build-out on top of the Phase 1 topic move. No behavior changes. Splits (existing content relocated, cross-linked): - queries/index.md → mutations/index.md (insert/update/delete + the inserts-vs-deletes rule) and search/index.md (the multi-modal search functions + a hybrid-ranking overview tying nearest/bm25/rrf together). queries/index.md now covers the read shape and points at both. - branching/index.md → branching/time-travel.md (snapshots/time travel) and branching/merge.md (three-way merge + the 7 conflict kinds, verified against error.rs MergeConflictKind). New pages (written from the code, user-facing): - quickstart.md — init → load → query → branch, with verified CLI flags. - concepts/index.md — what OmniGraph is + the L1/L2 (Lance/OmniGraph) framing. Expanded operations/audit.md from a 7-line struct dump into a real actor-tracking page (server token-resolved vs CLI --as chain; reading the trail; the omnigraph:recovery reserved actor). Index wiring: docs/user/index.md and AGENTS.md's topic table link every new page; also normalized AGENTS.md's docs/user link display text to match the Phase 1 retargeted paths. Verified: zero broken .md links; check-agents-md.sh green (57 links, 54 docs). Deferred to Phase 3: de-dev polish (grammar paths, IR internals still in queries/branching), guides/, and a possible reference/config.md split (the config schema is already coherent in cli/reference.md). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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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
Reading a branch at a past version, or a single entity at a past version, is covered on the time travel page. Merging branches and the conflict kinds are on the merge page.
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 five migrated writers (MutationStaging::finalize, schema_apply, branch_merge, ensure_indices, optimize_all_tables) 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.