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.

crates/omnigraph/src/loader/mod.rs

@@ -613,7 +613,7 @@ async fn load_jsonl_reader<R: BufRead>(
     } else {
         // LoadMode::Overwrite keeps the legacy inline-commit path —
         // truncate-then-append doesn't fit the staged shape (see
-        // `docs/runs.md` "LoadMode::Overwrite residual"). The recovery
+        // `docs/dev/writes.md` "LoadMode::Overwrite residual"). The recovery
         // sidecar is not applicable here because the writer doesn't go
         // through MutationStaging; per-table inline commits + a final
         // manifest publish handle their own residual via the documented