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/fixtures.py

@@ -10,7 +10,7 @@ import tempfile
 from pathlib import Path
 from typing import Any, Callable
 
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 def fixture_minimal_dict() -> dict[str, Any]:
@@ -62,16 +62,16 @@ def fixture_with_git_dict() -> dict[str, Any]:
     }
 
 
-def fixture_minimal() -> Manifest:
-    return Manifest.from_json_obj(fixture_minimal_dict())
+def fixture_minimal() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_minimal_dict())
 
 
-def fixture_with_egress() -> Manifest:
-    return Manifest.from_json_obj(fixture_with_egress_dict())
+def fixture_with_egress() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_with_egress_dict())
 
 
-def fixture_with_git() -> Manifest:
-    return Manifest.from_json_obj(fixture_with_git_dict())
+def fixture_with_git() -> ManifestIndex:
+    return ManifestIndex.from_json_obj(fixture_with_git_dict())
 
 
 def write_fixture(fn: Callable[[], dict[str, Any]]) -> Path: