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/runs.md

@@ -0,0 +1,38 @@
+# Runs (transactional graph mutations)
+
+`db/run_registry.rs` + run lifecycle in `db/omnigraph.rs`. Stored in `_graph_runs.lance` and `_graph_run_actors.lance`.
+
+## RunRecord
+
+```
+RunRecord {
+  run_id: RunId (ULID),
+  target_branch: String,           // where the run will publish
+  run_branch: "__run__<id>",       // ephemeral isolation branch
+  base_snapshot_id: String,
+  base_manifest_version: u64,
+  operation_hash: Option<String>,  // idempotency key
+  actor_id: Option<String>,
+  status: Running | Published | Failed | Aborted,
+  published_snapshot_id: Option<String>,
+  created_at, updated_at: i64 (microseconds),
+}
+```
+
+## Lifecycle
+
+1. `begin_run(target_branch, op_hash)` / `begin_run_as(target_branch, op_hash, actor_id)` — forks `__run__<id>` from the target's current head, appends a `RunRecord`.
+2. Mutations on `run_branch` (via the normal write APIs) — isolated from concurrent activity on the target.
+3. `publish_run(id)` / `publish_run_as(id, actor)`:
+   - **Fast path**: if the target hasn't moved since `base_snapshot_id`, promote the run snapshot directly.
+   - **Merge path**: if it has moved, perform a three-way merge (see [merge.md](merge.md)) into the target.
+   - On success: `status = Published`, `published_snapshot_id` set, run branch cleaned up asynchronously.
+4. `abort_run(id)` / `fail_run(id)` — terminal; cleans up run branch best-effort.
+
+## Idempotency
+
+`operation_hash` is an optional field clients can use to detect a duplicate `begin_run` retry.
+
+## Cleanup
+
+`cleanup_terminal_run_branches_for_target(branch)` is called as branches change; failures are swallowed (lazy cleanup on next branch op).