`copilot plugin install` from GitHub repo does not discover `.github/plugin/plugin.json` — skills and agents unavailable

[Megasware128]

Describe the bug

When installing a plugin directly from a GitHub repository using copilot plugin install <owner>/<repo>, the CLI downloads the full repository but sets cache_path in ~/.copilot/config.json to the repository root. The plugin loader then looks for plugin.json at the root of cache_path, but for repo-based plugins the plugin definition lives in .github/plugin/plugin.json.

As a result, skills and agents defined by the plugin are never loaded and do not appear in the available skills list.

Root Cause Analysis:

Comparing a working marketplace plugin (dotnet) with the direct install:

	Marketplace plugin (dotnet)	Direct repo install (winapp-cli)
cache_path	installed-plugins/awesome-copilot/dotnet	installed-plugins/_direct/microsoft--WinAppCli
plugin.json location	<cache_path>/plugin.json ✅	<cache_path>/.github/plugin/plugin.json ❌
Skills loaded	Yes	No

The marketplace plugin has a flattened structure with plugin.json at root. The direct repo install preserves the full repo structure where plugin.json lives in .github/plugin/.

Affected version

1.0.12

Steps to reproduce the behavior

1. Install a plugin from a GitHub repo: copilot plugin install microsoft/WinAppCli
2. Start a new Copilot CLI session
3. Check available skills (e.g. ask the agent to list skills, or check the system prompt)
4. Observe: winapp-cli skills and agents are not listed
5. Inspect ~/.copilot/config.json — cache_path points to repo root, not .github/plugin/

Expected behavior

The plugin loader should discover plugin.json inside .github/plugin/ for plugins installed from GitHub repositories. Skills and agents defined in the plugin should be available after installation.

Additional context

• OS: Windows 11
• Terminal: Windows Terminal
• Shell: PowerShell

Workaround: Manually edit ~/.copilot/config.json and append /.github/plugin to the cache_path:

"cache_path": "...\\microsoft--WinAppCli\\.github\\plugin"

After restarting the CLI, skills and agents are correctly discovered.

Suggested fix: When installing a plugin from a GitHub repo, the CLI should either:

1. Set cache_path to the .github/plugin/ subdirectory if plugin.json exists there, or
2. Have the plugin loader check .github/plugin/plugin.json as a fallback when plugin.json is not found at the cache_path root

Related issues in this repo:

• Installing plugins from a specific branch or tag #1296 — Mentions owner/repo:path/to/plugin install syntax which could serve as a workaround
• Support git symlinks in plugin install on Windows #2286 — Another plugin install issue on Windows (symlinks)
• Plugin skills installed by sessionStart hooks are not available in the current session #1855 — Plugin skills not available after sessionStart hook install (different root cause, same symptom)

Cross-repo notice

This issue has also been filed as microsoft/winappCli#365 since it affects the recommended install instructions in that repo's README. It is unclear whether the fix should be in the Copilot CLI (plugin loader not checking .github/plugin/), in the plugin repo (restructuring or adding a root-level plugin.json), or in both. Filing on both repos so the respective maintainers can determine the best course of action.