fix: sync CLI flags across analyze/pdf/unified commands and fix workflow JSON config

Flag/option synchronization fixes:
- analyze: add --dry-run, --api-key, and all workflow flags (--enhance-workflow,
  --enhance-stage, --var, --workflow-dry-run) via WORKFLOW_ARGUMENTS merge
- pdf: add --api-key to PDF_ARGUMENTS; replace 5 hardcoded add_argument() calls
  in pdf_scraper.py:main() with add_pdf_arguments() to activate all defined args
- unified: add --api-key and --enhance-level (global override) to UNIFIED_ARGUMENTS
  and standalone parser; wire enhance_level CLI override into run() per-source loop
- codebase_scraper: fix --enhance-workflow to use action="append" (was type=str),
  enabling multiple workflow chaining instead of silently dropping all but last

ConfigManager test isolation fix:
- __init__ now reads self.CONFIG_DIR/CONFIG_FILE/PROGRESS_DIR class variables
  instead of calling _get_config_dir()/_get_progress_dir() directly, enabling
  monkeypatching in tests (fixes pre-existing test_add_and_retrieve_github_profile)

Workflow JSON config support in unified_scraper:
- Phase 5 now reads workflows/workflow_stages/workflow_vars from top-level JSON
  config and merges them with CLI args (CLI-first ordering); supports running
  workflows even when unified scraper is called without CLI args (args=None)

Tests: 1,949 passed, 0 failed (added 18 new tests across 3 test files)

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

src/skill_seekers/cli/pdf_scraper.py

@@ -633,16 +633,14 @@ class PDFToSkillConverter:
 
 
 def main():
+    from .arguments.pdf import add_pdf_arguments
+
     parser = argparse.ArgumentParser(
         description="Convert PDF documentation to Claude skill",
         formatter_class=argparse.RawDescriptionHelpFormatter,
     )
 
-    parser.add_argument("--config", help="PDF config JSON file")
-    parser.add_argument("--pdf", help="Direct PDF file path")
-    parser.add_argument("--name", help="Skill name (with --pdf)")
-    parser.add_argument("--from-json", help="Build skill from extracted JSON")
-    parser.add_argument("--description", help="Skill description")
+    add_pdf_arguments(parser)
 
     args = parser.parse_args()