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_word_scraper.py

@@ -16,6 +16,7 @@ Tests cover:
 """
 
 import json
+import os
 import shutil
 import tempfile
 import unittest
@@ -456,6 +457,37 @@ class TestWordErrorHandling(unittest.TestCase):
         with self.assertRaises((KeyError, TypeError)):
             self.WordToSkillConverter({"docx_path": "test.docx"})
 
+    def test_non_docx_file_raises_value_error(self):
+        """extract_docx raises ValueError for non-.docx files."""
+        # Create a real file with wrong extension
+        txt_path = os.path.join(self.temp_dir, "test.txt")
+        with open(txt_path, "w") as f:
+            f.write("not a docx")
+        config = {"name": "test", "docx_path": txt_path}
+        converter = self.WordToSkillConverter(config)
+        with self.assertRaises(ValueError):
+            converter.extract_docx()
+
+    def test_doc_file_raises_value_error(self):
+        """extract_docx raises ValueError for .doc (old Word format)."""
+        doc_path = os.path.join(self.temp_dir, "test.doc")
+        with open(doc_path, "w") as f:
+            f.write("not a docx")
+        config = {"name": "test", "docx_path": doc_path}
+        converter = self.WordToSkillConverter(config)
+        with self.assertRaises(ValueError):
+            converter.extract_docx()
+
+    def test_no_extension_file_raises_value_error(self):
+        """extract_docx raises ValueError for file with no extension."""
+        no_ext_path = os.path.join(self.temp_dir, "document")
+        with open(no_ext_path, "w") as f:
+            f.write("not a docx")
+        config = {"name": "test", "docx_path": no_ext_path}
+        converter = self.WordToSkillConverter(config)
+        with self.assertRaises(ValueError):
+            converter.extract_docx()
+
 
 class TestWordJSONWorkflow(unittest.TestCase):
     """Test building skills from extracted JSON."""