feat(engine): sweep & remove legacy __run__ branch guard (MR-770) (#132)

* feat(engine): sweep legacy __run__ branches via v2→v3 manifest migration

Pre-v0.4.0 graphs can carry stale `__run__<id>` staging branches on the
`__manifest` dataset, left by the Run state machine removed in MR-771. Lance's
`list_branches` still enumerates them, so they leak into `branch_list()` and
count as blocking branches at schema-apply time.

Add a one-time `migrate_v2_to_v3` arm to the internal-schema dispatcher: on the
first read-write open it enumerates `__manifest` branches, deletes every
`__run__*` ref, and bumps the stamp to 3. Idempotent under retry (re-enumerates
fresh each run). The `"__run__"` prefix is inlined so the migration does not
depend on the run_registry guard that MR-770 removes next.

This is the prerequisite sweep; the guard removal follows in the next commit.

* refactor(engine): remove the legacy __run__ branch guard (MR-770)

With the v2→v3 migration sweeping stale `__run__*` branches off `__manifest`
on first read-write open, the defense-in-depth `is_internal_run_branch` guard
is no longer needed.

- delete `db/run_registry.rs`; drop the module + re-export from `db/mod.rs`
- collapse `is_internal_system_branch` to the schema-apply-lock check only
- `ensure_public_branch_ref`: drop the run-ref rejection; `__run__*` is now an
  ordinary branch name
- `branch_merge`: reject `is_internal_system_branch` (was run-only) so the
  schema-apply lock is rejected consistently with create/delete — a small,
  deliberate tightening
- update the inline schema-apply test + the writes integration tests
  (`public_branch_apis_reject_internal_run_refs` →
  `public_branch_apis_reject_internal_system_refs`, which also asserts
  `__run__*` now creates successfully)
- docs: flip the "pending production sweep / defense-in-depth" notes to
  "auto-swept by the v2→v3 migration"; document the read-only-open limitation

Known residual: the inert `_graph_runs.lance` / `_graph_run_actors.lance` bytes
remain until a `StorageAdapter::delete_prefix` primitive lands.

* fix(engine): run __run__ sweep at Omnigraph::open, not only on publish

Review (PR #132) caught a regression: removing __run__ from
`is_internal_system_branch` exposed legacy `__run__*` branches to the
schema-apply blocking-branch checks (schema_apply.rs:104 and :778) and to
`branch_list()`, but the v2→v3 sweep ran only inside the publisher's
`load_publish_state`. On a pre-v0.4.0 graph whose first write is a schema
apply, the blocking-branch check fires before any publish, so apply failed
with "found non-main branches: __run__…". The same lazy timing also created a
reverse hazard: a user-created `__run__*` branch on a still-v2 graph could be
deleted by the first publish's sweep.

Fix: run the internal-schema migration in `Omnigraph::open(ReadWrite)` (new
`manifest::migrate_on_open`), before the coordinator reads branch state. The
sweep now lands before any branch-observing code, and a graph is stamped v3 at
open — so the one-time sweep can never catch a legitimately-created branch.
Both checks and `branch_list` see the swept graph; correct by construction for
every write path.

Accepted residual: a read-only open of an unmigrated legacy graph still lists
`__run__*` (read-only opens must not write, so they can't sweep). Documented.

Regression test `legacy_run_branch_is_swept_on_open_and_does_not_block_schema_apply`
confirmed RED before the fix (panicked on the branch_list leak assertion) and
GREEN after. Also updates the stale schema_apply.rs comment, the writes.md
"Migration code" section, and adds the v3 row to storage.md's migration table.

* test(engine): sweep multiple legacy __run__ branches; doc nit

Strengthen the v2→v3 migration test to synthesize three `__run__*` branches
(a real legacy graph accumulates one per run) so the migration's delete loop
is exercised on a single reused dataset handle, not just a single branch.
Confirms multi-branch deletion is safe.

Also drop a stale "active runs" reference from the branch_delete doc line.

* fix(engine): force-delete in __run__ sweep for concurrency safety

`migrate_v2_to_v3` ran `Dataset::delete_branch` (= `branches().delete(.., false)`),
which errors "BranchContents not found" if the branch is already gone. Since the
sweep now runs in `Omnigraph::open(ReadWrite)`, two processes opening the same
legacy v2 graph concurrently would race: one wins each delete, the other's open
fails. The migration only claimed idempotency under *sequential* retry.

Switch to `Dataset::force_delete_branch` (= `delete(.., true)`), Lance's
documented path for cleaning up zombie branches, which tolerates an
already-absent branch. The sweep is now idempotent under concurrent runners and
robust to partial/zombie state. Found in self-review; no behavior change for the
common single-open path.

* docs(release): note MR-770 __run__ cleanup in v0.6.1

* docs(branches): reconcile branch cleanup semantics

docs/dev/writes.md

@@ -14,8 +14,11 @@ publisher's row-level CAS on `__manifest` is the single fence.
 
 - No `RunRecord`, no `_graph_runs.lance`, no `_graph_run_actors.lance`.
 - No `omnigraph run *` CLI subcommands and no `/runs/*` HTTP endpoints.
-- No `__run__<id>` staging branches. (Legacy on-disk artifacts from
-  pre-MR-771 repos are inert; MR-770 sweeps them in production.)
+- No `__run__<id>` staging branches; `__run__*` is no longer a reserved
+  name. The branch-name guard was removed in MR-770, and any stale
+  `__run__*` branch on an upgraded graph is swept off `__manifest` by the
+  v2→v3 internal-schema migration on first read-write open. (The inert
+  `_graph_runs.lance` bytes remain until a `delete_prefix` primitive lands.)
 - Cancelled mutation futures leave **no graph-level state** — only orphaned
   Lance fragments, which the existing `omnigraph cleanup` pipe reclaims.
 
@@ -245,9 +248,14 @@ list`.
 
 ## Migration code
 
-`db/manifest/migrations.rs` does not change. Active deletion of
-`_graph_runs.lance` belongs in MR-770 (the production sweep) — this PR
-stops *creating* run state but does not destroy legacy bytes on disk.
+`db/manifest/migrations.rs` carries the v2→v3 internal-schema step (MR-770):
+a one-time sweep that deletes legacy `__run__*` staging branches off
+`__manifest`. It runs in `Omnigraph::open(ReadWrite)` (via
+`manifest::migrate_on_open`, before the coordinator reads branch state) and
+again on the publisher's write path; both are idempotent once the stamp is at
+v3. Deleting the inert `_graph_runs.lance` / `_graph_run_actors.lance` dataset
+*bytes* is still deferred — it needs a `StorageAdapter::delete_prefix`
+primitive — but those bytes are invisible to graph-level state.
 
 ## Mid-query partial failure: closed by MR-794