fix: CI workflow improvements

- Fix installation test by using virtual environment instead of --system flag
- Run pre-commit hooks to fix formatting issues (trailing whitespace, end-of-file)

Author: prassanna-ravishankar

.cursor/rules/linting-philosophy.mdc

@@ -42,9 +42,9 @@ Only **truly global style choices** that apply project-wide:
 - `PLR0913` - Argument count (specific functions)
 
 ## Benefits
-✅ **Strict main code**: Source files enforce high quality standards  
-✅ **Appropriate flexibility**: Tests and examples have relaxed rules where needed  
-✅ **Clear rationale**: Each ignore is documented with specific reasoning  
+✅ **Strict main code**: Source files enforce high quality standards
+✅ **Appropriate flexibility**: Tests and examples have relaxed rules where needed
+✅ **Clear rationale**: Each ignore is documented with specific reasoning
 ✅ **Maintainable**: File-specific concerns handled at file level, not globally
 
 ## Verification

.cursor/rules/testing-philosophy.mdc

@@ -18,7 +18,7 @@ This project uses **behavioral (black-box) testing** instead of white-box testin
 - Test with realistic data scenarios
 
 ### ❌ DON'T: Test Internal Implementation
-- Avoid testing private methods directly  
+- Avoid testing private methods directly
 - Don't test internal data structures
 - Don't mock internal implementation details
 - Don't test "how" the code works, test "what" it does

.github/workflows/ci.yml

@@ -141,11 +141,14 @@ jobs:
       - name: Set up Python
         run: uv python install
 
+      - name: Create virtual environment
+        run: uv venv
+
       - name: Test wheel installation
-        run: uv pip install --system dist/*.whl
+        run: uv pip install dist/*.whl
 
       - name: Test package import
-        run: python -c "import clearml_mcp; print('✅ Package imported successfully')"
+        run: uv run python -c "import clearml_mcp; print('✅ Package imported successfully')"
 
       - name: Test CLI entry point
-        run: clearml-mcp --help || echo "✅ CLI entry point exists (may require ClearML config)" 
+        run: uv run clearml-mcp --help || echo "✅ CLI entry point exists (may require ClearML config)"

.pre-commit-config.yaml

@@ -18,4 +18,4 @@ repos:
       - id: ruff-format
 
   # Removed mypy from pre-commit due to dependency issues
-  # Type checking is handled separately in CI 
+  # Type checking is handled separately in CI

.specstory/.gitignore

@@ -0,0 +1,2 @@
+# SpecStory explanation file
+/.what-is-this.md