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/codebase_scraper.py

@@ -2406,9 +2406,10 @@ Examples:
     # Workflow enhancement arguments
     parser.add_argument(
         "--enhance-workflow",
-        type=str,
+        action="append",
         help=(
             "Enhancement workflow to use (name or path to YAML file). "
+            "Can be used multiple times to chain workflows. "
             "Examples: 'security-focus', 'architecture-comprehensive', "
             "'.skill-seekers/my-workflow.yaml'. "
             "Overrides --enhance-level when provided."