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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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- bundle luarocks source in the panto binary
- bootstrap process (intended for first `panto` run):
- make ~/.local/share/panto/...
- write out luarocks sources into it
- run luarocks to install luv
- new `panto bootstrap` command just runs the bootstrap
- `panto bootstrap --force` removes everything and re-bootstraps
- new `panto lua` command just runs panto's embedded lua
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- new multi-tool registration via ToolSource
- thread per source-or-standalone-tool
- switched to zig 0.16 Io threading interface
- cli: include `luv` package and run concurrent lua tools via libuv
- one single long-lived lua_State for the whole cli program
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