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/doc_scraper.py

@@ -47,28 +47,12 @@ from skill_seekers.cli.llms_txt_detector import LlmsTxtDetector
 from skill_seekers.cli.llms_txt_downloader import LlmsTxtDownloader
 from skill_seekers.cli.llms_txt_parser import LlmsTxtParser
 from skill_seekers.cli.arguments.scrape import add_scrape_arguments
+from skill_seekers.cli.utils import setup_logging
 
 # Configure logging
 logger = logging.getLogger(__name__)
 
 
-def setup_logging(verbose: bool = False, quiet: bool = False) -> None:
-    """Configure logging based on verbosity level.
-
-    Args:
-        verbose: Enable DEBUG level logging
-        quiet: Enable WARNING level logging only
-    """
-    if quiet:
-        level = logging.WARNING
-    elif verbose:
-        level = logging.DEBUG
-    else:
-        level = logging.INFO
-
-    logging.basicConfig(level=level, format="%(message)s", force=True)
-
-
 def infer_description_from_docs(
     base_url: str, first_page_content: str | None = None, name: str = ""
 ) -> str: