[BUG]: cluade Plugin.json + .apm directory in the same package causes apm install to delete the .apm directory

[abi-jey]

Describe the bug
When a package has both apm.yml and .claude-plugin/plugin.json with manifest paths pointing to .apm/ directories, apm install silently drops all agents and skills. The package appears in apm_modules/ but .apm/agents/ and .apm/skills/ are empty after install.

To Reproduce

1. Publish a package with this layout:
   packages/my-package/
   apm.yml
   .claude-plugin/plugin.json
   .apm/agents/my-agent.agent.md
   .apm/skills/my-skill/SKILL.md
   Where plugin.json references .apm/ paths:
   {
   "name": "my-package",
   "agents": [".apm/agents/my-agent.agent.md"],
   "skills": [".apm/skills/my-skill"]
   }
2. In a consumer project, run apm install
3. Install reports (files unchanged) — no agents or skills are integrated

Expected behavior
Agents and skills should be integrated normally:
[+] host/owner/repo/packages/my-package#v0.4.0 @9de7a012
|-- 1 agents integrated -> .github/agents/
|-- 1 skill(s) integrated -> .agents/skills/

Environment (please complete the following information):

• OS: macOS (Darwin)
• Python Version: 3.12.12
• APM Version: 0.12.4
• VSCode Version: N/A

Logs
[+] host/owner/repo/packages/my-package#v0.4.0 @9de7a012
|-- (files unchanged)

Additional context
Add any other context about the problem here.