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/github_scraper.py

@@ -31,6 +31,7 @@ except ImportError:
     sys.exit(1)
 
 from skill_seekers.cli.arguments.github import add_github_arguments
+from skill_seekers.cli.utils import setup_logging
 
 # Try to import pathspec for .gitignore support
 try:
@@ -40,8 +41,6 @@ try:
 except ImportError:
     PATHSPEC_AVAILABLE = False
 
-# Configure logging FIRST (before using logger)
-logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
 logger = logging.getLogger(__name__)
 
 # Import code analyzer for deep code analysis
@@ -1391,11 +1390,7 @@ def main():
     parser = setup_argument_parser()
     args = parser.parse_args()
 
-    # Set logging level from behavior args
-    if getattr(args, "quiet", False):
-        logging.getLogger().setLevel(logging.WARNING)
-    elif getattr(args, "verbose", False):
-        logging.getLogger().setLevel(logging.DEBUG)
+    setup_logging(verbose=getattr(args, "verbose", False), quiet=getattr(args, "quiet", False))
 
     # Handle --dry-run
     if getattr(args, "dry_run", False):