fix(types): add BottleSpec.loaded_manifest to satisfy pyright on union type

BottleSpec.manifest is ManifestIndex | Manifest (pre/post _validate()).
Downstream code always runs post-validate so it needs Manifest, but
pyright flagged every .agent/.bottle access. The new loaded_manifest
property asserts isinstance and returns Manifest, giving pyright a
narrowed type without scattering type: ignore everywhere.

Also remove unused Manifest imports from test files and annotate the
_index() helper in test_manifest_agent_git_user.

bot_bottle/contrib/codex/agent_provider.py

@@ -177,7 +177,7 @@ class CodexAgentProvider(AgentProvider):
         skills."""
         from ...backend.util import host_skill_dir
 
-        agent = plan.spec.manifest.agent
+        agent = plan.spec.loaded_manifest.agent
         if not agent.skills:
             return
         skills_dir = _skills_dir(plan.guest_home)
@@ -206,7 +206,7 @@ class CodexAgentProvider(AgentProvider):
             f"chown node:node {prompt_path} && chmod 600 {prompt_path}",
             user="root",
         )
-        agent = plan.spec.manifest.agent
+        agent = plan.spec.loaded_manifest.agent
         return prompt_path if plan.agent_provision.has_prompt or agent.prompt else None
 
     def provision(self, plan: "BottlePlan", bottle: "Bottle") -> None: