chore: Fix formatting and exclude mkdocs.yml from YAML check

- Exclude mkdocs.yml from check-yaml (uses custom YAML constructors)
- Run black, isort, ruff on all files for consistency
- Fix formatting in agents/epic_integration_wizard.py
- Fix formatting in empathy_software_plugin/cli.py
- Fix formatting in examples/debugging_assistant.py
- Fix formatting in tests/test_secrets_detector.py

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Co-Authored-By: Claude <[email protected]>

Author: 2 people

.pre-commit-config.yaml

@@ -56,6 +56,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        exclude: mkdocs.yml  # Uses custom YAML constructors
       - id: check-added-large-files
         args: ['--maxkb=1000']
       - id: check-merge-conflict