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/integration/test_macos_container_launch.py

@@ -29,7 +29,7 @@ from bot_bottle.backend.macos_container.util import (
     dns_server as _container_dns_server,
     is_available as _container_available,
 )
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 
 
 _AGENT_PROMPT = "You are a launch smoke-test agent. Be brief."
@@ -52,8 +52,8 @@ def _minimal_agent_dockerfile(path: Path) -> None:
     )
 
 
-def _minimal_manifest(dockerfile: Path) -> Manifest:
-    return Manifest.from_json_obj({
+def _minimal_manifest(dockerfile: Path) -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "agent_provider": {

tests/integration/test_sandbox_escape.py

@@ -31,7 +31,7 @@ from pathlib import Path
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
 from bot_bottle.bottle_state import cleanup_state
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
@@ -101,7 +101,7 @@ class TestSandboxEscape(unittest.TestCase):
         cls._key_path.write_text("placeholder\n")
         cls._key_path.chmod(0o600)
 
-        manifest = Manifest.from_json_obj({
+        manifest = ManifestIndex.from_json_obj({
             "bottles": {
                 "dev": {
                     # Three fake secrets — different shapes — land

tests/integration/test_sidecar_bundle_compose.py

@@ -22,15 +22,15 @@ from pathlib import Path
 from unittest.mock import patch
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
-def _manifest() -> Manifest:
+def _manifest() -> ManifestIndex:
     """Bottle with supervise on so the bundle exercises egress +
     supervise. Git is off because a meaningful git-gate test needs
     a real upstream and SSH keys — out of scope for a bundle smoke."""
-    return Manifest.from_json_obj({
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "supervise": True,

tests/integration/test_smolmachines_launch.py

@@ -35,15 +35,15 @@ from pathlib import Path
 
 from bot_bottle.backend import BottleSpec, get_bottle_backend
 from bot_bottle.backend.smolmachines.smolvm import is_available as _smolvm_available
-from bot_bottle.manifest import Manifest
+from bot_bottle.manifest import ManifestIndex
 from tests._docker import skip_unless_docker
 
 
 _AGENT_PROMPT = "You are demo. Be brief."
 
 
-def _minimal_manifest() -> Manifest:
-    return Manifest.from_json_obj({
+def _minimal_manifest() -> ManifestIndex:
+    return ManifestIndex.from_json_obj({
         "bottles": {
             "dev": {
                 "egress": {