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/resume.py

@@ -20,7 +20,7 @@ import argparse
 from ..backend import BottleSpec
 from ..bottle_state import read_metadata
 from ..log import die
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 from .start import _launch_bottle
 
@@ -42,7 +42,7 @@ def cmd_resume(argv: list[str]) -> int:
             f"check ~/.bot-bottle/state/ or run `cli.py start` to create a new bottle"
         )
 
-    manifest = Manifest.resolve(USER_CWD)
+    manifest = ManifestIndex.resolve(USER_CWD)
     manifest.require_agent(metadata.agent_name)
 
     spec = BottleSpec(