Plugin update button grayed out / doesn't pull new directories added after initial install

Summary

When a plugin that was previously installed receives new top-level directories (e.g., an agents/ directory added in a later commit), the Update mechanism fails to create those new directories on the user's machine. The Update button becomes grayed out (indicating the system believes the installed copy is current), but the new directories are absent. The only workaround is to Remove and Reinstall the plugin.

Steps to Reproduce

1. Install a plugin from the marketplace that has skills/ and commands/ directories but no agents/ directory
2. The plugin vendor pushes new commits adding an agents/ directory with agent .md files
3. The marketplace version is bumped and synced
4. In the plugin browser, open the plugin detail page and check for updates
5. The Update button becomes grayed out even though the agents/ directory is not present locally
6. Agents do not appear in /agents selector or anywhere in the Claude Code interface

Expected Behavior

• Update button should be active when new directories/files have been added to the plugin
• OR the Update mechanism should fully sync the plugin directory tree, including creating new directories
• Users should not need to Remove + Reinstall to get new plugin components

Actual Behavior

• Update button shows as grayed out ("already up to date") after marketplace sync
• The agents/ directory is missing from the local plugin cache
• Agents from the plugin do not appear anywhere in the Claude Code interface
• Workaround: Remove the plugin and Reinstall from the marketplace

Environment

• Claude Code (latest)
• Plugin installed from a marketplace (GitHub-hosted marketplace.json)
• Plugin is a monorepo with multiple plugins referenced via source: paths in marketplace.json

Additional Context

We noticed this while adding 74 AI agents across 34 MSP plugins in msp-claude-plugins. All agents were added after users had already installed the plugins. The marketplace was updated with new version numbers and synced successfully (the synced commit hash updated in the UI), but the Update button was grayed out for all plugins and agents were not visible.

The specific pattern that seems to trigger this:

• Plugin initially installed with: skills/, commands/, .claude-plugin/
• New commit adds: agents/ directory with agent .md files
• Update mechanism syncs the commit hash but does not materialize the new agents/ directory