refactor(manifest): consolidate the manifest modules into a bot_bottle.manifest package

Move the nine root-level manifest modules into a bot_bottle/manifest/ package,
dropping the redundant manifest_ prefix: the facade (manifest.py) becomes the
package __init__ and keeps re-exporting Manifest / ManifestIndex and the piece
types, while manifest_<x>.py become manifest/<x>.py (agent, bottle, egress,
extends, git, loader, schema, util).

Because the facade stays the package __init__, the ~13 callers that import
`from bot_bottle.manifest import ...` are unchanged; only direct-piece imports
move to `bot_bottle.manifest.<name>`. Inside the package, intra-manifest
imports drop the prefix and the non-manifest siblings (log, yaml_subset,
agent_provider) move to `..`.

No behavior change; full unit suite green.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

tests/unit/test_cli_start_selector.py

@@ -336,7 +336,7 @@ class TestManifestToYaml(unittest.TestCase):
         agent_provider_template: str = "claude",
     ):
         from bot_bottle.manifest import Manifest, ManifestBottle
-        from bot_bottle.manifest_agent import ManifestAgent, ManifestAgentProvider
+        from bot_bottle.manifest.agent import ManifestAgent, ManifestAgentProvider
 
         agent = ManifestAgent(skills=tuple(skills))
         bottle = ManifestBottle(

tests/unit/test_git_gate_render_provision.py

@@ -21,7 +21,7 @@ from bot_bottle.git_gate import (
     git_gate_render_gitconfig,
     revoke_git_gate_provisioned_keys,
 )
-from bot_bottle.manifest_git import ManifestGitEntry, ManifestKeyConfig
+from bot_bottle.manifest.git import ManifestGitEntry, ManifestKeyConfig
 
 
 def _entry(**kw: Any) -> ManifestGitEntry:

tests/unit/test_manifest_bottle_merge.py

@@ -14,7 +14,7 @@ import unittest
 from pathlib import Path
 
 from bot_bottle.manifest import ManifestBottle, ManifestError, ManifestIndex
-from bot_bottle.manifest_extends import merge_bottles_runtime
+from bot_bottle.manifest.extends import merge_bottles_runtime
 
 
 def _index(bottles: dict[str, object], agents: dict[str, object]) -> ManifestIndex:
@@ -44,7 +44,7 @@ class TestMergeBottlesRuntime(unittest.TestCase):
         self.assertEqual("y", result.env["ONLY_OVERRIDE"])
 
     def test_egress_routes_concatenated(self):
-        from bot_bottle.manifest_egress import ManifestEgressConfig, ManifestEgressRoute
+        from bot_bottle.manifest.egress import ManifestEgressConfig, ManifestEgressRoute
         r1 = ManifestEgressRoute(Host="api.a.com")
         r2 = ManifestEgressRoute(Host="api.b.com")
         base = ManifestBottle(egress=ManifestEgressConfig(routes=(r1,)))

tests/unit/test_manifest_validation.py

@@ -14,12 +14,12 @@ from unittest.mock import patch
 from bot_bottle.env import resolve_env
 from bot_bottle.errors import MissingEnvVarError
 from bot_bottle.manifest import Manifest, ManifestBottle, ManifestIndex
-from bot_bottle.manifest_agent import (
+from bot_bottle.manifest.agent import (
     ManifestAgent,
     ManifestAgentProvider,
     _parse_provider_settings,
 )
-from bot_bottle.manifest_util import ManifestError
+from bot_bottle.manifest.util import ManifestError
 
 
 def _idx(obj: dict[str, object]) -> ManifestIndex: