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>

src/skill_seekers/cli/adaptors/faiss_helpers.py

@@ -11,6 +11,7 @@ from pathlib import Path
 from typing import Any
 
 from .base import SkillAdaptor, SkillMetadata
+from skill_seekers.cli.arguments.common import DEFAULT_CHUNK_TOKENS, DEFAULT_CHUNK_OVERLAP_TOKENS
 
 
 class FAISSHelpers(SkillAdaptor):
@@ -81,6 +82,7 @@ class FAISSHelpers(SkillAdaptor):
                     "file": "SKILL.md",
                     "type": "documentation",
                     "version": metadata.version,
+                    "doc_version": metadata.doc_version,
                 }
 
                 # Chunk if enabled
@@ -88,9 +90,10 @@ class FAISSHelpers(SkillAdaptor):
                     content,
                     doc_metadata,
                     enable_chunking=enable_chunking,
-                    chunk_max_tokens=kwargs.get("chunk_max_tokens", 512),
+                    chunk_max_tokens=kwargs.get("chunk_max_tokens", DEFAULT_CHUNK_TOKENS),
                     preserve_code_blocks=kwargs.get("preserve_code_blocks", True),
                     source_file="SKILL.md",
+                    chunk_overlap_tokens=kwargs.get("chunk_overlap_tokens", DEFAULT_CHUNK_OVERLAP_TOKENS),
                 )
 
                 # Add all chunks to parallel arrays
@@ -110,6 +113,7 @@ class FAISSHelpers(SkillAdaptor):
                     "file": ref_file.name,
                     "type": "reference",
                     "version": metadata.version,
+                    "doc_version": metadata.doc_version,
                 }
 
                 # Chunk if enabled
@@ -117,9 +121,10 @@ class FAISSHelpers(SkillAdaptor):
                     ref_content,
                     doc_metadata,
                     enable_chunking=enable_chunking,
-                    chunk_max_tokens=kwargs.get("chunk_max_tokens", 512),
+                    chunk_max_tokens=kwargs.get("chunk_max_tokens", DEFAULT_CHUNK_TOKENS),
                     preserve_code_blocks=kwargs.get("preserve_code_blocks", True),
                     source_file=ref_file.name,
+                    chunk_overlap_tokens=kwargs.get("chunk_overlap_tokens", DEFAULT_CHUNK_OVERLAP_TOKENS),
                 )
 
                 # Add all chunks to parallel arrays
@@ -155,8 +160,9 @@ class FAISSHelpers(SkillAdaptor):
         skill_dir: Path,
         output_path: Path,
         enable_chunking: bool = False,
-        chunk_max_tokens: int = 512,
+        chunk_max_tokens: int = DEFAULT_CHUNK_TOKENS,
         preserve_code_blocks: bool = True,
+        chunk_overlap_tokens: int = DEFAULT_CHUNK_OVERLAP_TOKENS,
     ) -> Path:
         """
         Package skill into JSON file for FAISS.
@@ -176,12 +182,8 @@ class FAISSHelpers(SkillAdaptor):
         output_path = self._format_output_path(skill_dir, Path(output_path), "-faiss.json")
         output_path.parent.mkdir(parents=True, exist_ok=True)
 
-        # Read metadata
-        metadata = SkillMetadata(
-            name=skill_dir.name,
-            description=f"FAISS data for {skill_dir.name}",
-            version="1.0.0",
-        )
+        # Read metadata from SKILL.md frontmatter
+        metadata = self._build_skill_metadata(skill_dir)
 
         # Generate FAISS data
         faiss_json = self.format_skill_md(
@@ -190,6 +192,7 @@ class FAISSHelpers(SkillAdaptor):
             enable_chunking=enable_chunking,
             chunk_max_tokens=chunk_max_tokens,
             preserve_code_blocks=preserve_code_blocks,
+            chunk_overlap_tokens=chunk_overlap_tokens,
         )
 
         # Write to file