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>

uv.lock

@@ -3621,11 +3621,11 @@ wheels = [
 
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+dependencies = [
+    { name = "certifi" },
+    { name = "orjson" },
+    { name = "pinecone-plugin-assistant" },
+    { name = "pinecone-plugin-interface" },
+    { name = "python-dateutil" },
+    { name = "typing-extensions" },
+    { name = "urllib3" },
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+
 [[package]]
 name = "platformdirs"
 version = "4.9.2"
@@ -5405,6 +5445,7 @@ all = [
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     { name = "numpy", version = "2.4.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
     { name = "openai" },
+    { name = "pinecone" },
     { name = "python-docx" },
     { name = "sentence-transformers" },
     { name = "sse-starlette" },
@@ -5457,8 +5498,12 @@ mcp = [
 openai = [
     { name = "openai" },
 ]
+pinecone = [
+    { name = "pinecone" },
+]
 rag-upload = [
     { name = "chromadb" },
+    { name = "pinecone" },
     { name = "sentence-transformers" },
     { name = "weaviate-client" },
 ]
@@ -5533,6 +5578,9 @@ requires-dist = [
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     { name = "pathspec", specifier = ">=0.12.1" },
     { name = "pillow", specifier = ">=11.0.0" },
+    { name = "pinecone", marker = "extra == 'all'", specifier = ">=5.0.0" },
+    { name = "pinecone", marker = "extra == 'pinecone'", specifier = ">=5.0.0" },
+    { name = "pinecone", marker = "extra == 'rag-upload'", specifier = ">=5.0.0" },
     { name = "pydantic", specifier = ">=2.12.3" },
     { name = "pydantic-settings", specifier = ">=2.11.0" },
     { name = "pygithub", specifier = ">=2.5.0" },
@@ -5563,7 +5611,7 @@ requires-dist = [
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     { name = "weaviate-client", marker = "extra == 'weaviate'", specifier = ">=3.25.0" },
 ]
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+provides-extras = ["mcp", "gemini", "openai", "all-llms", "s3", "gcs", "azure", "docx", "chroma", "weaviate", "sentence-transformers", "pinecone", "rag-upload", "all-cloud", "embedding", "all"]
 
 [package.metadata.requires-dev]
 dev = [