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/info.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import argparse
 
 from ..log import info
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD
 
 
@@ -14,12 +14,12 @@ def cmd_info(argv: list[str]) -> int:
     parser.add_argument("name", help="agent name defined in bot-bottle.json")
     args = parser.parse_args(argv)
 
-    names = Manifest.resolve(USER_CWD)
+    names = ManifestIndex.resolve(USER_CWD)
     names.require_agent(args.name)
     manifest = names.load_for_agent(args.name)
 
-    agent = manifest.agents[args.name]
-    bottle = manifest.bottle_for(args.name)
+    agent = manifest.agent
+    bottle = manifest.bottle
     env_names = list(bottle.env.keys())
     prompt_first_line = agent.prompt.splitlines()[0] if agent.prompt else ""
 
@@ -32,7 +32,7 @@ def cmd_info(argv: list[str]) -> int:
         f"first line: {prompt_first_line or '(empty)'}"
     )
     info(f"bottle             : {agent.bottle}")
-    identity = manifest.git_identity_summary(args.name)
+    identity = manifest.git_identity_summary()
     if identity:
         info(f"  git identity  : {identity}")
     if bottle.git:

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

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(

bot_bottle/cli/start.py

@@ -33,7 +33,7 @@ from ..bottle_state import (
 )
 # from ..backend.docker.capability_apply import snapshot_transcript
 from ..log import info
-from ..manifest import Manifest
+from ..manifest import ManifestIndex
 from ._common import PROG, USER_CWD, read_tty_line
 from . import tui
 
@@ -62,7 +62,7 @@ def cmd_start(argv: list[str]) -> int:
 
     dry_run = args.dry_run or os.environ.get("BOT_BOTTLE_DRY_RUN") == "1"
 
-    manifest = Manifest.resolve(USER_CWD)
+    manifest = ManifestIndex.resolve(USER_CWD)
 
     agent_name: str | None = args.name
     if agent_name is None: