fix: plugin agents not deployed due to directory nesting bug

[danielmeppiel]

Problem

When plugin.json declares agents as a custom list (e.g. "agents": ["./agents"]), _map_plugin_artifacts preserved the directory name, creating .apm/agents/agents/ instead of .apm/agents/. This caused agent files to be silently dropped during integration — they never reached the AgentIntegrator.

Real-world impact: The context-engineering plugin from github/awesome-copilot has a context-architect.md agent that was never deployed to .github/agents/.

Root Cause

Unlike skills (which are named directories containing SKILL.md), agents are flat files — each .md is one agent. The custom-list branch in _map_plugin_artifacts was using copytree(d, target / d.name) which nests the directory, but should use copytree(d, target) to merge contents directly — matching how the non-custom (default) path already worked.

Changes

Fix 1 — plugin_parser.py (root cause)

Agents custom-list branch now merges directory contents into .apm/agents/ directly instead of preserving the directory name as a subdirectory.

Fix 2 — agent_integrator.py (defensive)

Changed glob() → rglob() in find_agent_files so agents in subdirectories are still discovered even if nesting occurs from other sources.

Fix 3 — plugin.py (consistency)

Plugin.from_path only discovered *.agent.md files. Now also discovers plain .md files (excluding known non-agent names like README.md), matching what AgentIntegrator.find_agent_files already does.

Tests

• Updated test_mixed_files_and_dirs to assert flattened (correct) behavior
• Added test_custom_agents_dir_list_flattens_contents — regression test for the exact context-engineering plugin pattern
• Added test_find_agent_files_discovers_nested_subdirectories — validates rglob resilience
• Added test_get_target_filename_plain_md — confirms .md → .agent.md rename for .github/agents/

Verification

• All 1729 tests pass, 0 regressions
• End-to-end: apm install in sample project now correctly deploys context-architect.agent.md to .github/agents/

[Copilot]

Pull request overview

Fixes plugin agent deployment when plugin.json uses a custom agents directory list (e.g. "agents": ["./agents"]), ensuring mapped agent files end up where AgentIntegrator can discover and integrate them.

Changes:

• Flatten agent directory contents into .apm/agents/ in plugin artifact mapping to avoid .apm/agents/agents/ nesting.
• Make AgentIntegrator.find_agent_files() resilient to nested agent directories by switching glob() → rglob().
• Expand plugin agent discovery to include plain .md files under agents/ (not only *.agent.md), plus add/adjust regression tests.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/apm_cli/deps/plugin_parser.py	Fixes agent mapping so custom agent directories are merged directly into .apm/agents/.
src/apm_cli/integration/agent_integrator.py	Switches to recursive discovery for .apm/agents to avoid silent drops when nesting occurs.
src/apm_cli/models/plugin.py	Broadens Plugin.from_path() agent discovery to include plain .md files.
tests/unit/test_plugin_parser.py	Updates/extends mapping tests to assert flattened agents behavior and prevent regression.
tests/unit/integration/test_agent_integrator.py	Adds tests for nested agent discovery and plain .md → .agent.md target naming.

[Copilot]

Docs appear to be out of sync with this change: docs/plugins.md currently states that when a custom component path array contains directories, each directory is preserved as a named subdirectory. With this update agents directories are always flattened into .apm/agents/ (no agents/<dir-name>/ nesting). Please update docs/plugins.md to clarify that agents are an exception (flattened), while skills keep the named-subdir behavior.

[danielmeppiel]

Good catch — fixed in afb01d6. docs/plugins.md now clarifies that agents are flattened into .apm/agents/ while skills keep the named-subdirectory behavior.