docs: rename runs.md/runs.rs → writes and repoint all references (#131)

The Run state machine was removed in MR-771 (v0.4.0); `docs/dev/runs.md`
and `crates/omnigraph/tests/runs.rs` have since documented and tested the
direct-publish write path, so the "runs" name was misleading.

- git mv docs/dev/runs.md → docs/dev/writes.md (reframe H1 + intro;
  keep MR-771 history note)
- git mv crates/omnigraph/tests/runs.rs → tests/writes.rs (reframe header)
- repoint every runs.md / runs.rs reference across docs, AGENTS.md, and
  source comments
- fix four pre-existing broken `docs/runs.md` links (the file never lived
  at that path) to `docs/dev/writes.md`
- fix the stale v0.4.0 anchor to the live section

No behavior change: every source edit is a comment. Engine builds and the
renamed test passes 25/25; scripts/check-agents-md.sh passes.

The run-removal cleanup itself (run_registry.rs guard, __run__ prefix) is
deferred to MR-770.

docs/dev/index.md

@@ -21,7 +21,7 @@ constraints. User-facing behavior should still be documented through
 |---|---|
 | System structure, L1/L2 framing, component diagrams | [architecture.md](architecture.md) |
 | On-disk layout, manifest schema, URI behavior | [storage.md](../user/storage.md) |
-| Direct-publish writes, D2, staged writes, recovery sidecars | [runs.md](runs.md) |
+| Direct-publish writes, D2, staged writes, recovery sidecars | [writes.md](writes.md) |
 | Query execution, mutation execution, loader flow | [execution.md](execution.md) |
 | Index lifecycle and graph topology indexes | [indexes.md](../user/indexes.md) |
 | Branch and commit internals | [branches-commits.md](../user/branches-commits.md) |