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Replace all references to the "system" layer with "base" to better reflect
its role as the foundational extension/tool layer in panto's hierarchy.
The layer hierarchy now consistently uses: project > user > base.
Includes:
- Update agent README and build.zig documentation
- Refactor tool registry and config module to support layered lookups
- Add TestHarness abstraction for cleaner test setup
- Improve JSON serialization with wire-encoded tool names
- Add glob pattern matching for tool/extension discovery
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