Fix quality gates and maintainability

[gabeorlanski]

Summary

• Resolve Ty and Ruff findings across the repository and add Ty, Ruff, Vulture, and Pytest to the local pre-commit gate.
• Split Claude trace handling and MiniSWE integration into focused modules, remove legacy debug fixture adapters, and simplify resume prompt validation.
• Restore MiniSWE agent registration by removing the package/module shadowing and add a regression test.
• Narrow protocol loading failures to expected dependency-loading errors.

Why

The previous code mixed adapter behavior into agent modules, retained dead legacy fixture hooks, and allowed the MiniSWE agent implementation to be shadowed by its parser package. The new structure keeps third-party patching and artifact schemas at explicit boundaries while preserving existing behavior.

Validation

• uv run pre-commit run --all-files (Ruff, Ty, Vulture, Pytest)
• Full pytest -q suite (1,670 tests collected)
• Focused regression suite: 87 passed
• Real Docker validation of Claude trace cleanup permissions (0400 → owner-only 0600)