fix: resolve 18 bugs and code quality issues across adaptors, CLI, and chunking pipeline

Bug fixes:
- Fix --var flag silently dropped in create routing (args.workflow_var → args.var)
- Fix double _score_code_quality() call in word scraper
- Add .docx file extension validation in WordToSkillConverter
- Fix weaviate ImportError masked by generic Exception handler
- Fix RAG chunking crash using non-existent converter.output_dir

Chunking pipeline improvements:
- Wire --chunk-overlap-tokens through entire package pipeline
  (package_skill → adaptor.package → format_skill_md → _maybe_chunk_content → RAGChunker)
- Add auto-scaling overlap: max(50, chunk_tokens//10) when chunk size is non-default
- Rename --no-preserve-code to --no-preserve-code-blocks (backward-compat alias kept)
- Replace hardcoded 512/50 chunk defaults with DEFAULT_CHUNK_TOKENS/DEFAULT_CHUNK_OVERLAP_TOKENS
  constants across all 12 concrete adaptors, rag_chunker, base, and package_skill

Code quality:
- Extract shared _generate_openai_embeddings() and _generate_st_embeddings() to SkillAdaptor
  base class, removing ~150 lines of duplication from chroma/weaviate/pinecone
- Add Pinecone adaptor with full upload support (pinecone_adaptor.py)

Tests (14 new):
- chunk_overlap_tokens parameter wiring, auto-scaling overlap, preserve_code_blocks flag
- .docx/.doc/no-extension file validation, --var flag routing E2E
- Embedding method inheritance verification, backward-compatible flag aliases

Docs:
- Update CHANGELOG, CLI_REFERENCE, API_REFERENCE, packaging guide (EN+ZH)
- Update README test count badge (1880+ → 2283+)

All 2283 tests passing, 8 skipped, 0 failures.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/test_create_arguments.py

@@ -25,8 +25,8 @@ class TestUniversalArguments:
     """Test universal argument definitions."""
 
     def test_universal_count(self):
-        """Should have exactly 18 universal arguments (after Phase 2 workflow integration + local_repo_path)."""
-        assert len(UNIVERSAL_ARGUMENTS) == 18
+        """Should have exactly 19 universal arguments (after Phase 2 workflow integration + local_repo_path + doc_version)."""
+        assert len(UNIVERSAL_ARGUMENTS) == 19
 
     def test_universal_argument_names(self):
         """Universal arguments should have expected names."""
@@ -50,6 +50,7 @@ class TestUniversalArguments:
             "var",
             "workflow_dry_run",
             "local_repo_path",  # GitHub local clone path for unlimited C3.x analysis
+            "doc_version",  # Documentation version tag for RAG metadata
         }
         assert set(UNIVERSAL_ARGUMENTS.keys()) == expected_names
 
@@ -130,7 +131,7 @@ class TestArgumentHelpers:
         """Should return set of universal argument names."""
         names = get_universal_argument_names()
         assert isinstance(names, set)
-        assert len(names) == 18  # Phase 2: added 4 workflow arguments + local_repo_path
+        assert len(names) == 19  # Phase 2: added 4 workflow arguments + local_repo_path + doc_version
         assert "name" in names
         assert "enhance_level" in names  # Phase 1: consolidated flag
         assert "enhance_workflow" in names  # Phase 2: workflow support