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_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: