refactor(manifest): split Manifest into ManifestIndex + Manifest single-value type

Manifest now holds exactly one agent and one effective bottle (with
git_user overlay already applied). The old multi-agent/bottle
collection is renamed ManifestIndex. BottleSpec.manifest starts as
ManifestIndex from the CLI and becomes Manifest after _validate()
calls load_for_agent(); all provisioning code downstream reads
spec.manifest.agent / spec.manifest.bottle instead of indexing by name.

tests/unit/test_plan_print_parity.py

@@ -19,14 +19,14 @@ from bot_bottle.backend.docker.bottle_plan import DockerBottlePlan
 from bot_bottle.backend.smolmachines.bottle_plan import SmolmachinesBottlePlan
 from bot_bottle.egress import EgressPlan, EgressRoute
 from bot_bottle.git_gate import GitGatePlan, GitGateUpstream
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import Manifest, ManifestIndex
 
 
 def _manifest() -> Manifest:
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {"dev": {}},
         "agents": {"demo": {"skills": [], "prompt": "", "bottle": "dev"}},
-    })
+    }).load_for_agent("demo")
 
 
 def _spec(manifest: Manifest, tmp: str) -> BottleSpec: