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.

bot_bottle/cli/list.py

@@ -7,7 +7,7 @@ import os
 import sys
 
 from ..backend import enumerate_active_agents
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 
 _ANSI_COLOR_CODES: dict[str, str] = {
@@ -40,7 +40,7 @@ def cmd_list(argv: list[str]) -> int:
     args = parser.parse_args(argv)
 
     if args.scope == "available":
-        manifest = Manifest.resolve(USER_CWD)
+        manifest = ManifestIndex.resolve(USER_CWD)
         for name in manifest.all_agent_names:
             print(name)
         return 0