[FEATURE] Plugin user override layer — preserve local customizations across plugin updates

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

When a user installs a plugin and customizes a skill to fit their workflow —
adjusting prompts, adding org-specific context, tweaking behavior — those
changes are silently overwritten the next time they run /plugin to update.
There is no diff, no merge step, and no warning. The user must either avoid
updating or manually back up and reapply their changes every time.

Concrete scenario:

1. User installs ai-pm-copilot from a team marketplace
2. User modifies ~/.claude/plugins/ai-pm-copilot/skills/prd-templates/SKILL.md
3. Plugin maintainer ships a new version with improvements to prd-templates
4. User runs /plugin to get the improvements
5. Their customizations are gone — overwritten with no indication

Proposed Solution

A user override layer: a parallel directory (e.g. ~/.claude/plugins-user/)
where users place files that shadow installed plugin files at load time, without
modifying the plugin directory itself.

• /plugin updates only touch ~/.claude/plugins/ — the user layer is never modified
• If a matching file exists in ~/.claude/plugins-user/<plugin-name>/, it takes

precedence at load time

• Customizations survive all future updates

This is the same pattern used by VS Code (user settings over default settings),
Linux .d/ drop-in directories, and browser user scripts.

Alternative Solutions

Option A: Warn before overwriting user-modified files — at least prevents
silent data loss, even without solving the merge problem.

Option B: Show a diff and prompt for merge on update — similar to how
Debian's dpkg handles .conf file conflicts.

Option C: A user-overrides/ directory inside the plugin install that
/plugin is instructed never to touch.

Priority

Medium - Would be very helpful

Feature Category

Configuration and settings

Use Case Example

_No response_

Additional Context

_No response_