fix: resolve all ruff linting errors (W293, F401, B904, UP007, UP045, E741, SIM102, SIM117, ARG)

Auto-fixed (whitespace, imports, type annotations):
- codebase_scraper.py: W293 blank lines with whitespace
- doc_scraper.py: W293 blank lines with whitespace
- parsers/extractors/__init__.py: W293
- parsers/extractors/base_parser.py: W293, UP007, UP045, F401

Manual fixes:
- enhancement_workflow.py: B904 raise without `from exc`, remove unused `os` import
- parsers/extractors/quality_scorer.py: E741 ambiguous var `l` → `line`
- parsers/extractors/rst_parser.py: SIM102 nested if → combined conditions (x2)
- pdf_scraper.py: F821 undefined `logger` → `print()` (consistent with file style)
- mcp/tools/workflow_tools.py: ARG001 unused `args` → `_args`
- tests/test_workflow_runner.py: ARG005 unused lambda args → `_a`/`_kw`, ARG001 `kwargs` → `_kwargs`
- tests/test_workflows_command.py: SIM117 nested with → combined with (x2)

All 1922 tests pass.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

tests/test_create_integration_basic.py

@@ -122,28 +122,28 @@ class TestCreateCommandArgvForwarding:
 
     def _make_args(self, **kwargs):
         import argparse
-        defaults = dict(
-            enhance_workflow=None,
-            enhance_stage=None,
-            var=None,
-            workflow_dry_run=False,
-            enhance_level=0,
-            output=None,
-            name=None,
-            description=None,
-            config=None,
-            api_key=None,
-            dry_run=False,
-            verbose=False,
-            quiet=False,
-            chunk_for_rag=False,
-            chunk_size=512,
-            chunk_overlap=50,
-            preset=None,
-            no_preserve_code_blocks=False,
-            no_preserve_paragraphs=False,
-            interactive_enhancement=False,
-        )
+        defaults = {
+            "enhance_workflow": None,
+            "enhance_stage": None,
+            "var": None,
+            "workflow_dry_run": False,
+            "enhance_level": 0,
+            "output": None,
+            "name": None,
+            "description": None,
+            "config": None,
+            "api_key": None,
+            "dry_run": False,
+            "verbose": False,
+            "quiet": False,
+            "chunk_for_rag": False,
+            "chunk_size": 512,
+            "chunk_overlap": 50,
+            "preset": None,
+            "no_preserve_code_blocks": False,
+            "no_preserve_paragraphs": False,
+            "interactive_enhancement": False,
+        }
         defaults.update(kwargs)
         return argparse.Namespace(**defaults)