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>

docs/branches-commits.md

@@ -0,0 +1,51 @@
+# 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 name `main`; fails if branch exists; ensures the schema-apply lock is idle.
+- `branch_list()` — returns public branches, **filters internal** `__run__…` and `__schema_apply_lock__` prefixes.
+- `branch_delete(name)` — refuses if there are descendants or active runs on the branch; cleans up owned per-branch fragments.
+- **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.
+- `sync_branch(branch)` — re-binds the in-memory handle to the latest head of the branch.
+
+## L2 — Commit graph (`db/commit_graph.rs`)
+
+Stored as a Lance dataset `_graph_commits.lance` (with stable row IDs):
+
+```
+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>,
+  created_at: i64 (microseconds since epoch),
+}
+```
+
+- Every successful publish (load / change / merge / schema_apply / publish_run) appends one commit.
+- Merge commits have two parents; linear commits have one.
+- `_graph_commit_actors.lance` — optional separate actor map (created on demand).
+- 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 a `ReadTarget` (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 `Snapshot` is a `(version, HashMap<table_key, SubTableEntry>)` — cheap to build, snapshot-isolated cross-table reads.
+
+## L2 — Internal system branches
+
+Filtered from `branch_list()` but visible to internals:
+
+- `__run__<run-id>` — ephemeral isolation branch for a transactional run.
+- `__schema_apply_lock__` — serializes schema migrations.