docs: update README and add pixi-based tests

- Add property-based tests for PixiRunner
- Add HAN055.fna test data file
- Update README with pixi installation and usage guide
- Update .gitignore for pixi and test artifacts
- Update CLI to remove Docker-related arguments

.gitignore

@@ -5,6 +5,7 @@ __pycache__/
 .Python
 venv/
 *.egg-info/
+.venv/
 
 # Node
 node_modules/
@@ -28,7 +29,21 @@ tests/test_data/genomes/*.fna
 .idea/
 *.swp
 
-.venv/
+# Test/Build artifacts
+.pytest_cache/
+.hypothesis/
+htmlcov/
+.coverage
 
+# Pipeline outputs
 runs/
-tests/output
+tests/output/
+tests/logs/
+
+# Pixi (keep .pixi but ignore lock in subprojects)
+.pixi/envs/
+
+# uv lock (optional, can be committed for reproducibility)
+# uv.lock
+
+.kiro