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/utils.py

@@ -17,6 +17,22 @@ logger = logging.getLogger(__name__)
 T = TypeVar("T")
 
 
+def setup_logging(verbose: bool = False, quiet: bool = False) -> None:
+    """Configure root logging level based on verbosity flags.
+
+    Args:
+        verbose: Enable DEBUG level logging
+        quiet: Enable WARNING level logging only (suppress INFO)
+    """
+    if quiet:
+        level = logging.WARNING
+    elif verbose:
+        level = logging.DEBUG
+    else:
+        level = logging.INFO
+    logging.basicConfig(level=level, format="%(message)s", force=True)
+
+
 def open_folder(folder_path: str | Path) -> bool:
     """
     Open a folder in the system file browser