fix(plugin): prevent _map_plugin_artifacts from destroying pre-positioned .apm/ content

[abi-jey]

Summary

Fixes #1415

When a package has both apm.yml and .claude-plugin/plugin.json with manifest paths pointing into .apm/, apm install silently drops all agents and skills — reporting (files unchanged).

Root Cause

detect_package_type classifies packages with .claude-plugin/plugin.json as MARKETPLACE_PLUGIN (cascade priority — checked before APM_PACKAGE), even when apm.yml is present. This triggers _validate_marketplace_plugin → normalize_plugin_directory → _map_plugin_artifacts.

_map_plugin_artifacts is designed for pure plugins where agents/ and skills/ sit at the package root and need to be copied INTO .apm/. It does a shutil.rmtree on the target (.apm/agents/, .apm/skills/) before copying from the source. When the manifest points to paths already inside .apm/, the source and target overlap — the rmtree destroys the source before the copy can read it.

Sequence:

1. Download copies package to apm_modules/ — .apm/agents/ and .apm/skills/ are present
2. validate_apm_package → _map_plugin_artifacts runs
3. shutil.rmtree(.apm/agents/) — deletes the source
4. shutil.copy2(source_file, ...) — source no longer exists, nothing is copied
5. Integrate phase finds empty .apm/ → (files unchanged)

Fix

Added _all_inside_apm() helper that detects when all resolved source paths already reside under .apm/. When true, the destructive rmtree+copy cycle is skipped — the artifacts are already correctly positioned. Applied to all four component types: agents, skills, commands, hooks.

Tests

5 new regression tests in TestMapPluginArtifactsPrePositioned:

• test_agents_inside_apm_are_preserved — manifest agents pointing into .apm/ survive
• test_skills_inside_apm_are_preserved — manifest skills pointing into .apm/ survive
• test_commands_inside_apm_are_preserved — manifest commands pointing into .apm/ survive
• test_hooks_inside_apm_are_preserved — manifest hooks pointing into .apm/ survive
• test_external_agents_still_copied — normal root-level→.apm/ copy still works (non-regression)

All 4 regression tests fail without the fix, pass with it. All 73 plugin parser tests pass.

[Copilot]

Pull request overview

Fixes a destructive edge case in plugin artifact normalization during apm install when plugin.json component paths point into an already-populated .apm/ tree, preventing accidental deletion of pre-positioned agents/skills/prompts/hooks.

Changes:

• Added a containment guard in _map_plugin_artifacts() to skip the rmtree + copy cycle when sources appear to already live under .apm/.
• Added regression tests ensuring .apm/ content is preserved for agents, skills, commands (prompts), and hooks.
• Added a non-regression test confirming root-level agents/ are still copied into .apm/agents/.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
src/apm_cli/deps/plugin_parser.py	Adds _all_inside_apm() and uses it to conditionally skip destructive remapping for agents/skills/commands/hooks.
tests/unit/test_plugin_parser.py	Adds regression coverage for pre-positioned .apm/ artifact preservation and one non-regression copy test.