Finer plugin control

### Describe the feature or problem you'd like to solve

Currenlty all plugins are installed globally at $HOME/.copilot/installed-plugins. Which makes it up the to user to make sure they have disabled at repo level via settings.json. Ideally users should be able to disable all plugins globally, via the global settings.json($HOME/.copilot/settings.json) and just toggle the plugin they need at repo level.

### Proposed solution

_No response_

### Example prompts or workflows

_No response_

### Additional context

_No response_

Review the plugin directory at $HOME/.copilot/installed-plugins and the global and repository settings.json files. Trace how plugin enablement is currently determined, then define and verify behavior where global settings disable plugins by default and repository settings selectively enable them.

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