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>

pyproject.toml

@@ -128,10 +128,15 @@ sentence-transformers = [
     "sentence-transformers>=2.2.0",
 ]
 
+pinecone = [
+    "pinecone>=5.0.0",
+]
+
 rag-upload = [
     "chromadb>=0.4.0",
     "weaviate-client>=3.25.0",
     "sentence-transformers>=2.2.0",
+    "pinecone>=5.0.0",
 ]
 
 # All cloud storage providers combined
@@ -167,6 +172,7 @@ all = [
     "azure-storage-blob>=12.19.0",
     "chromadb>=0.4.0",
     "weaviate-client>=3.25.0",
+    "pinecone>=5.0.0",
     "fastapi>=0.109.0",
     "sentence-transformers>=2.3.0",
     "numpy>=1.24.0",