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_workflow_tools_mcp.py

@@ -9,7 +9,6 @@ Covers:
 """
 
 import textwrap
-from pathlib import Path
 from unittest.mock import patch
 
 import pytest
@@ -290,7 +289,7 @@ class TestDeleteWorkflowTool:
         wf.write_text(MINIMAL_YAML, encoding="utf-8")
 
         with _mock_bundled_names([]):
-            result = delete_workflow_tool({"name": "my-wf"})
+            delete_workflow_tool({"name": "my-wf"})
 
         assert not wf.exists()