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/contrib/codex/agent_provider.py

@@ -177,7 +177,7 @@ class CodexAgentProvider(AgentProvider):
         skills."""
         from ...backend.util import host_skill_dir
 
-        agent = plan.spec.manifest.agents[plan.spec.agent_name]
+        agent = plan.spec.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.agents[plan.spec.agent_name]
+        agent = plan.spec.manifest.agent
         return prompt_path if plan.agent_provision.has_prompt or agent.prompt else None
 
     def provision(self, plan: "BottlePlan", bottle: "Bottle") -> None: