fix: resolve issue #299 and Phase 1 cleanup

- Fix #299: rename --chunk-size/--chunk-overlap to --streaming-chunk-size/
  --streaming-overlap in arguments/package.py to avoid collision with the
  RAG --chunk-size flag from arguments/common.py
- Phase 1a: make package_skill.py import args via add_package_arguments()
  instead of a 105-line inline duplicate argparse block; fixes the root
  cause of _reconstruct_argv() passing unrecognised flag names
- Phase 1b: centralise setup_logging() into utils.py and remove 4
  duplicate module-level logging.basicConfig() calls from doc_scraper.py,
  github_scraper.py, codebase_scraper.py, and unified_scraper.py
- Fix test_package_structure.py / test_cli_paths.py version strings
  (3.1.1 → 3.1.2)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/skill_seekers/cli/unified_scraper.py

@@ -28,12 +28,12 @@ try:
     from skill_seekers.cli.conflict_detector import ConflictDetector
     from skill_seekers.cli.merge_sources import ClaudeEnhancedMerger, RuleBasedMerger
     from skill_seekers.cli.unified_skill_builder import UnifiedSkillBuilder
+    from skill_seekers.cli.utils import setup_logging
 except ImportError as e:
     print(f"Error importing modules: {e}")
     print("Make sure you're running from the project root directory")
     sys.exit(1)
 
-logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
 logger = logging.getLogger(__name__)
 
 
@@ -1134,6 +1134,7 @@ Examples:
     )
 
     args = parser.parse_args()
+    setup_logging()
 
     # Create scraper
     scraper = UnifiedScraper(args.config, args.merge_mode)