refactor(#1173): defer agents-kind descriptor declarations (option a)

Adopt maintainer-recommended option (a): keep the convertedAgentsKind /
stageAgentsForRuntimeWithConverter scope-threading plumbing, but DEFER the
8 runtimes' capability.json `agents`-kind declarations to a follow-up that
first ships the ADR-1235 §0 byte-for-byte parity harness.

The declarations were a live regression: the second `layout.kinds` consumer,
applySurface / `/gsd:surface` / `--materialize` (src/surface.cts), does not
mirror the legacy agent pipeline (copilot `.agent.md` rename, path-prefix
rewrite + attribution, stale cleanup), so a `/gsd:surface` toggle deleted
installed copilot `gsd-*.agent.md` and path-unrewrote the other 7 runtimes.
trek-e + davesienkowski both flagged this.

- Revert the agents-kind entries from the 8 capability.json files and
  regenerate capability-registry.cjs (now matches next; 0 converted agents
  kinds declared).
- Revert the declaration-driven kind-count test bumps
  (runtime-artifact-layout, descriptor-drive, bug-782, enh-789, enh-790).
- Keep the synthetic-descriptor seam tests for convertedAgentsKind dispatch;
  add a synthetic scope-threading test so the kept isGlobal plumbing stays
  covered without depending on real declarations.
- Update the convertedAgentsKind doc comment to state declarations are
  deferred pending the ADR-1235 §0 parity harness.
- Move ADR-1235 to Accepted.
- Reword the changeset to plumbing-only (docs-exempt now honest: no runtime
  declares the kind, legacy loop authoritative, installed output unchanged).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

tests/enh-789-codebuddy-commands.test.cjs

@@ -53,12 +53,11 @@ const RESOLVED_CORE = resolveProfile({ modes: ['core'], manifest: MANIFEST });
 // ─── Layout contract ─────────────────────────────────────────────────────────
 
 describe('enh-789 — codebuddy layout has commands + skills kinds', () => {
-  test('resolveRuntimeArtifactLayout codebuddy returns 3 kinds', () => {
-    // #1173: codebuddy gained an agents kind (descriptor-driven per-runtime agent conversion).
+  test('resolveRuntimeArtifactLayout codebuddy returns 2 kinds', () => {
     const layout = resolveRuntimeArtifactLayout('codebuddy', '/tmp/fake-codebuddy-dir');
-    assert.strictEqual(layout.kinds.length, 3, 'codebuddy must have exactly 3 artifact kinds');
+    assert.strictEqual(layout.kinds.length, 2, 'codebuddy must have exactly 2 artifact kinds');
     const kindNames = layout.kinds.map(k => k.kind).sort();
-    assert.deepStrictEqual(kindNames, ['agents', 'commands', 'skills']);
+    assert.deepStrictEqual(kindNames, ['commands', 'skills']);
   });
 
   test('codebuddy commands kind targets commands/ with gsd- prefix', () => {