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/codebase_scraper.py

@@ -37,6 +37,7 @@ from skill_seekers.cli.code_analyzer import CodeAnalyzer
 from skill_seekers.cli.config_extractor import ConfigExtractor
 from skill_seekers.cli.dependency_analyzer import DependencyAnalyzer
 from skill_seekers.cli.signal_flow_analyzer import SignalFlowAnalyzer
+from skill_seekers.cli.utils import setup_logging
 
 # Try to import pathspec for .gitignore support
 try:
@@ -46,8 +47,6 @@ try:
 except ImportError:
     PATHSPEC_AVAILABLE = False
 
-# Configure logging
-logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
 logger = logging.getLogger(__name__)
 
 
@@ -2382,11 +2381,7 @@ Examples:
     if args.depth is None:
         args.depth = "deep"  # Default depth
 
-    # Set logging level
-    if getattr(args, "quiet", False):
-        logging.getLogger().setLevel(logging.WARNING)
-    elif args.verbose:
-        logging.getLogger().setLevel(logging.DEBUG)
+    setup_logging(verbose=args.verbose, quiet=getattr(args, "quiet", False))
 
     # Handle --dry-run
     if getattr(args, "dry_run", False):