Support path negation with custom instructions applyTo paths

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

I want to provide broad instructions that apply to 90% of our monorepo. However they do not apply to a small subset. Rather than having to add every single path they DO apply to (hundreds), I want to be able to specify certain paths they do NOT apply to

### Proposed solution

Support negation pattern like:
```
applyTo: **/*.cpp, !/but/not/this/path/**
```

### Example prompts or workflows

I want to provide broad instructions that apply to 90% of our monorepo. However they do not apply to a small subset. Rather than having to add every single path they DO apply to (hundreds), I want to be able to specify certain paths they do NOT apply to

### Additional context

_No response_

The issue names custom instructions' applyTo paths and proposes a negated pattern such as `! /but/not/this/path/**`. Start by locating the applyTo path-matching entry point and its existing pattern tests. Done means broad patterns still apply while explicitly negated paths are excluded.

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