[WIP] Fix linter errors to enable checks

[Copilot]

Plan to Fix Linter Errors

• Investigate linter errors (688 total errors found)
• Run linter with auto-fix for safe fixes (117 errors fixed: 688 → 571)
• Review and commit auto-fixed errors
• Fix major error categories (571 → 448 errors):
  • T201: print statements (41 occurrences) - replaced with logging
  • G004: logging format strings (35 occurrences) - converted to %s format
  • B023: function definition issues in loops (16 occurrences) - added default arguments
  • B904: raise from None issues (13 occurrences) - added from e/None
  • B006: mutable default arguments (13 occurrences) - changed to None pattern
  • S607: shell commands without full path (8 occurrences) - added noqa
  • E741: ambiguous variable names (6 occurrences) - renamed variables
  • N818: exception name conventions (5 occurrences) - renamed exceptions
  • A001/A002/A004: shadowing builtins (10 occurrences) - added noqa for third-party code
• Fix remaining 20 critical errors (type comparisons, unused imports, naming conventions, etc.)
• Address remaining 448 stylistic errors (mostly LOG015, TRY003, FA102, EM102, TID252)
• Run tests to ensure no functionality is broken
• Enable linter check in CI workflow

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-taskflow-agent/.github/workflows/ci.yml

Line 38 in d4d4acd

# 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.</issue_description>

<agent_instructions>Fix all of the linter errors. Do not disable the rules.</agent_instructions>

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

• Fixes Fix linter errors #83

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