Fix .gitignore to allow docs files and add documentation files

- Fix .gitignore pattern: un-ignore docs/ directory first, then ignore docs/*, then un-ignore specific files
- Add all documentation files referenced in README.md:
  - USAGE_GUIDE.md
  - CONFIGURATION_GUIDE.md
  - TEST_SCENARIOS.md
  - MODULES.md
  - DEVELOPER_FAQ.md
  - PUBLISHING.md
  - CONTRIBUTING.md
  - API_SPECIFICATION.md
  - TESTING_GUIDE.md
  - IMPLEMENTATION_CHECKLIST.md
- Pre-commit hooks fixed trailing whitespace and end-of-file formatting

.gitignore

@@ -109,8 +109,11 @@ flakestorm.yaml
 secrets/
 
 # docs (exclude all, but allow specific files referenced in README)
-docs/
-# Allow docs files referenced in README.md
+# First, un-ignore the docs directory itself
+!docs/
+# Then ignore all files in docs
+docs/*
+# Now un-ignore the specific files we want to track
 !docs/USAGE_GUIDE.md
 !docs/CONFIGURATION_GUIDE.md
 !docs/TEST_SCENARIOS.md