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>

tests/test_cli_paths.py

@@ -138,7 +138,7 @@ class TestUnifiedCLIEntryPoints(unittest.TestCase):
 
             # Should show version
             output = result.stdout + result.stderr
-            self.assertIn("3.1.1", output)
+            self.assertIn("3.1.2", output)
 
         except FileNotFoundError:
             # If skill-seekers is not installed, skip this test

tests/test_package_structure.py

@@ -24,7 +24,7 @@ class TestCliPackage:
         import skill_seekers.cli
 
         assert hasattr(skill_seekers.cli, "__version__")
-        assert skill_seekers.cli.__version__ == "3.1.1"
+        assert skill_seekers.cli.__version__ == "3.1.2"
 
     def test_cli_has_all(self):
         """Test that skill_seekers.cli package has __all__ export list."""
@@ -88,7 +88,7 @@ class TestMcpPackage:
         import skill_seekers.mcp
 
         assert hasattr(skill_seekers.mcp, "__version__")
-        assert skill_seekers.mcp.__version__ == "3.1.1"
+        assert skill_seekers.mcp.__version__ == "3.1.2"
 
     def test_mcp_has_all(self):
         """Test that skill_seekers.mcp package has __all__ export list."""
@@ -108,7 +108,7 @@ class TestMcpPackage:
         import skill_seekers.mcp.tools
 
         assert hasattr(skill_seekers.mcp.tools, "__version__")
-        assert skill_seekers.mcp.tools.__version__ == "3.1.1"
+        assert skill_seekers.mcp.tools.__version__ == "3.1.2"
 
 
 class TestPackageStructure:
@@ -212,7 +212,7 @@ class TestRootPackage:
         import skill_seekers
 
         assert hasattr(skill_seekers, "__version__")
-        assert skill_seekers.__version__ == "3.1.1"
+        assert skill_seekers.__version__ == "3.1.2"
 
     def test_root_has_metadata(self):
         """Test that skill_seekers root package has metadata."""