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/user/transactions.md

@@ -164,5 +164,5 @@ This is the workflow MR-797 / agentic loops are designed around: **branches are
 - [`docs/user/branches-commits.md`](branches-commits.md) — branch and commit-graph mechanics.
 - [`docs/dev/merge.md`](../dev/merge.md) — three-way merge details and conflict kinds.
 - [`docs/user/query-language.md`](query-language.md) — `.gq` syntax for the multi-statement queries used above.
-- [`docs/dev/runs.md`](../dev/runs.md) — the per-query commit pipeline that gives single-query atomicity.
+- [`docs/dev/writes.md`](../dev/writes.md) — the per-query commit pipeline that gives single-query atomicity.
 - [`docs/dev/invariants.md`](../dev/invariants.md) — the architectural rule.