refactor: rename all chunk flags to include explicit units

Replace ambiguous --chunk-size / --chunk-overlap names that meant different
things in different contexts (tokens vs characters) with fully explicit names:

- --chunk-size (RAG tokens)     → --chunk-tokens
- --chunk-overlap (RAG tokens)  → --chunk-overlap-tokens
- --chunk (enable RAG chunking) → --chunk-for-rag
- --streaming-chunk-size (chars) → --streaming-chunk-chars
- --streaming-overlap (chars)    → --streaming-overlap-chars
- --chunk-size (PDF pages)       → --pdf-pages-per-chunk (poc file)

Also aligns stream_parser.py help with streaming_ingest.py standalone parser.
All 2167 tests pass.

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

tests/test_chunking_integration.py

@@ -291,7 +291,7 @@ class TestChunkingCLIIntegration:
     """Test chunking via CLI arguments."""
 
     def test_chunk_flag(self, tmp_path):
-        """Test --chunk flag enables chunking."""
+        """Test --chunk-for-rag flag enables chunking."""
         from skill_seekers.cli.package_skill import package_skill
 
         skill_dir = create_test_skill(tmp_path, large_doc=True)
@@ -301,7 +301,7 @@ class TestChunkingCLIIntegration:
             open_folder_after=False,
             skip_quality_check=True,
             target="langchain",
-            enable_chunking=True,  # --chunk flag
+            enable_chunking=True,  # --chunk-for-rag flag
             chunk_max_tokens=512,
             preserve_code_blocks=True,
         )

tests/test_cli_refactor_e2e.py

@@ -32,8 +32,8 @@ class TestParserSync:
             ["skill-seekers", "scrape", "--help"], capture_output=True, text=True
         )
         assert "--chunk-for-rag" in result.stdout, "Help should show --chunk-for-rag flag"
-        assert "--chunk-size" in result.stdout, "Help should show --chunk-size flag"
-        assert "--chunk-overlap" in result.stdout, "Help should show --chunk-overlap flag"
+        assert "--chunk-tokens" in result.stdout, "Help should show --chunk-tokens flag"
+        assert "--chunk-overlap-tokens" in result.stdout, "Help should show --chunk-overlap-tokens flag"
 
     def test_scrape_verbose_flag_works(self):
         """Test that --verbose flag (previously missing) now works."""

tests/test_create_arguments.py

@@ -40,8 +40,8 @@ class TestUniversalArguments:
             "verbose",
             "quiet",
             "chunk_for_rag",
-            "chunk_size",
-            "chunk_overlap",  # Phase 2: RAG args from common.py
+            "chunk_tokens",
+            "chunk_overlap_tokens",  # Phase 2: RAG args from common.py
             "preset",
             "config",
             # Phase 2: Workflow arguments (universal workflow support)