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/maintenance.md

@@ -0,0 +1,22 @@
+# Maintenance: Optimize & Cleanup
+
+`db/omnigraph/optimize.rs`.
+
+## `optimize_all_tables(db)` — non-destructive
+
+- Lance `compact_files()` on every node + edge table on `main`.
+- Rewrites small fragments into fewer large ones; old fragments remain reachable via older manifests.
+- Bounded by `OMNIGRAPH_MAINTENANCE_CONCURRENCY` (default 8).
+- Returns `[TableOptimizeStats { table_key, fragments_removed, fragments_added, committed }]`.
+
+## `cleanup_all_tables(db, options)` — destructive
+
+- Lance `cleanup_old_versions()` per table.
+- Removes manifests (and their unique fragments) older than the retention policy.
+- `CleanupPolicyOptions { keep_versions: Option<u32>, older_than: Option<Duration> }` — at least one is required.
+- Returns `[TableCleanupStats { table_key, bytes_removed, old_versions_removed }]`.
+- CLI guards with `--confirm`; without it, prints a preview line.
+
+## Tombstones
+
+Logical sub-table delete markers in `__manifest`; `tombstone_object_id(table_key, version)` excludes a sub-table version from snapshot reconstruction.