Fix linter errors and enable linter check in CI

[Copilot]

• Explore repository structure and understand codebase
• Run hatch fmt auto-fix (fixed 60 of 293 errors initially)
• Add missing __init__.py files to mcp_servers/ and mcp_servers/codeql_python/ directories
• Configure ruff in pyproject.toml to ignore acceptable patterns:
  • E402: Module imports not at top (logging config before imports)
  • FBT001/FBT002: Boolean positional arguments (common in API design)
  • N802: Uppercase function names (for acronyms like GHSA)
  • RUF013: Implicit Optional type hints
  • A001/A002/A003: Shadowing builtins (next, id, etc.)
  • TID252: Relative imports (acceptable within same package)
  • And other minor style preferences
• Fix remaining code issues:
  • Convert set([...]) to set literals {...}
  • Rename unused loop variables with _ prefix
  • Fix non-breaking space character in comment
  • Remove unused variable assignments
  • Convert list comprehension to set comprehension
• Run hatch fmt to auto-format all files (14 files reformatted)
• Update CI workflow to enable hatch fmt --check
• Verify tests still pass
• Run code review and CodeQL security check - no new issues introduced
• Resolve merge conflict with main branch (took main's Field descriptions + applied formatting)
• Resolve second round of merge conflicts with PR Use seclab_taskflow_agent.path_utils #11 (path_utils changes) + applied linter fixes

Original prompt

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This section details on the original issue you should resolve

<issue_title>Fix linter errors</issue_title>
<issue_description>I switched off the linter because it produces 100s of error messages:

seclab-taskflows/.github/workflows/ci.yml

Line 38 in 8f81d69

# hatch fmt --check

We should fix those errors (or find a way to suppress them if they're uninteresting), so that we can switch the check on.

Note: this is the same problem as GitHubSecurityLab/seclab-taskflow-agent#83</issue_description>

<agent_instructions>Run hatch fmt --check on the repo and fix all the errors that it finds.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Fix linter errors #8

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[kevinbackhouse]

@copilot : please resolve the merge conflicts

[Copilot]

@copilot : please resolve the merge conflicts

Resolved the merge conflict in repo_context.py. I took the main branch's version (which has Field descriptions added to function parameters) and applied the linter formatting. The changes are in commit 2164a1a.

[kevinbackhouse]

@copilot : please resolve the merge conflicts

[Copilot]

@copilot : please resolve the merge conflicts

Resolved all merge conflicts from PR #11 (path_utils changes). I took main's version with the mcp_data_dir and log_file_name utilities and applied linter formatting. The changes are in commit cbe81c5.