chore: remove dead code and temporary files

- Delete unused thought_processor_refactored.py (200 lines of dead code)
- Delete AGNO_2.2.12_MIGRATION.md (migration complete, info in CLAUDE.md)
- Delete CONTINUATION_SUMMARY.md (temporary session notes)
- Simplify run_command() in run_tests.py (10 lines → 3 lines)
- Run ruff autofix and format (100+ style issues resolved)
- Clean Python cache directories

Removes approximately 740 lines of unused/temporary code and improves
code quality across the codebase.

Author: FradSer

.gitignore

@@ -12,3 +12,8 @@ wheels/
 
 # Testing
 .hypothesis/
+.pytest_cache/
+.coverage
+htmlcov/
+.coverage.*
+test-results.xml