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>

tests/test_analyze_command.py

@@ -181,5 +181,89 @@ class TestAnalyzePresetBehavior(unittest.TestCase):
         self.assertFalse(args.comprehensive)
 
 
+class TestAnalyzeWorkflowFlags(unittest.TestCase):
+    """Test workflow and parity flags added to the analyze subcommand."""
+
+    def setUp(self):
+        """Create parser for testing."""
+        self.parser = create_parser()
+
+    def test_enhance_workflow_accepted_as_list(self):
+        """Test --enhance-workflow is accepted and stored as a list."""
+        args = self.parser.parse_args(
+            ["analyze", "--directory", ".", "--enhance-workflow", "security-focus"]
+        )
+        self.assertEqual(args.enhance_workflow, ["security-focus"])
+
+    def test_enhance_workflow_chained_twice(self):
+        """Test --enhance-workflow can be chained to produce a two-item list."""
+        args = self.parser.parse_args(
+            [
+                "analyze",
+                "--directory",
+                ".",
+                "--enhance-workflow",
+                "security-focus",
+                "--enhance-workflow",
+                "minimal",
+            ]
+        )
+        self.assertEqual(args.enhance_workflow, ["security-focus", "minimal"])
+
+    def test_enhance_stage_accepted_as_list(self):
+        """Test --enhance-stage is accepted with action=append."""
+        args = self.parser.parse_args(
+            ["analyze", "--directory", ".", "--enhance-stage", "sec:Analyze security"]
+        )
+        self.assertEqual(args.enhance_stage, ["sec:Analyze security"])
+
+    def test_var_accepted_as_list(self):
+        """Test --var is accepted with action=append (dest is 'var')."""
+        args = self.parser.parse_args(
+            ["analyze", "--directory", ".", "--var", "focus=performance"]
+        )
+        self.assertEqual(args.var, ["focus=performance"])
+
+    def test_workflow_dry_run_flag(self):
+        """Test --workflow-dry-run sets the flag."""
+        args = self.parser.parse_args(
+            ["analyze", "--directory", ".", "--workflow-dry-run"]
+        )
+        self.assertTrue(args.workflow_dry_run)
+
+    def test_api_key_stored_correctly(self):
+        """Test --api-key is stored in args."""
+        args = self.parser.parse_args(
+            ["analyze", "--directory", ".", "--api-key", "sk-ant-test"]
+        )
+        self.assertEqual(args.api_key, "sk-ant-test")
+
+    def test_dry_run_stored_correctly(self):
+        """Test --dry-run is stored in args."""
+        args = self.parser.parse_args(["analyze", "--directory", ".", "--dry-run"])
+        self.assertTrue(args.dry_run)
+
+    def test_workflow_flags_combined(self):
+        """Test workflow flags can be combined with other analyze flags."""
+        args = self.parser.parse_args(
+            [
+                "analyze",
+                "--directory",
+                ".",
+                "--enhance-workflow",
+                "security-focus",
+                "--api-key",
+                "sk-ant-test",
+                "--dry-run",
+                "--enhance-level",
+                "1",
+            ]
+        )
+        self.assertEqual(args.enhance_workflow, ["security-focus"])
+        self.assertEqual(args.api_key, "sk-ant-test")
+        self.assertTrue(args.dry_run)
+        self.assertEqual(args.enhance_level, 1)
+
+
 if __name__ == "__main__":
     unittest.main()