fix(generate): report unreferenced tools

[happykawayigt]

Summary

• preserve the complete top-level tool registry in the compiled system spec
• report tools that are declared but not referenced by any agent as ignore
• keep ignored tools out of generated stubs and plugins.toml
• cover direct generator behavior and first/idempotent CLI runs

Fixes #67

Validation

• targeted regression tests: 2 passed
• full pytest excluding five existing Windows path-separator assertions in tests/generate/test_plugins_manifest.py: 555 passed
• mypy src tests: 169 source files passed
• Ruff check and format check for all changed files
• git diff --check

AI assistance

Implemented and reviewed with OpenAI Codex; all listed validation commands were run locally.

[AmitAvital1]

Hi @happykawayigt please see discord message and follow this instructions

[Asaf-prog]

Thanks, this looks good and matches the intended behavior from #67.

The implementation keeps the complete top-level tool registry in SystemSpec, reports tools that are declared but not referenced by the compiled agent graph, and correctly avoids generating stubs or manifest entries for them.

The CLI output is clear, and I like that the tests cover both the initial generation and the idempotent second run.

One small non-blocking suggestion: since the PR also guarantees that ignored tools stay out of plugins.toml, it would be useful to add an explicit assertion for that in the generator test.

Otherwise, the scope and implementation look good to me. Once it is ready, please mark the PR as ready for review.