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/arguments/analyze.py

@@ -10,6 +10,8 @@ Includes preset system support for #268.
 import argparse
 from typing import Any
 
+from .workflow import WORKFLOW_ARGUMENTS
+
 ANALYZE_ARGUMENTS: dict[str, dict[str, Any]] = {
     # Core options
     "directory": {
@@ -169,8 +171,27 @@ ANALYZE_ARGUMENTS: dict[str, dict[str, Any]] = {
             "help": "Enable verbose logging",
         },
     },
+    # Dry-run and API key (parity with scrape/github/pdf)
+    "dry_run": {
+        "flags": ("--dry-run",),
+        "kwargs": {
+            "action": "store_true",
+            "help": "Preview what will be analyzed without creating output",
+        },
+    },
+    "api_key": {
+        "flags": ("--api-key",),
+        "kwargs": {
+            "type": str,
+            "help": "Anthropic API key (or set ANTHROPIC_API_KEY env var)",
+            "metavar": "KEY",
+        },
+    },
 }
 
+# Add workflow arguments (enhance_workflow, enhance_stage, var, workflow_dry_run, workflow_history)
+ANALYZE_ARGUMENTS.update(WORKFLOW_ARGUMENTS)
+
 
 def add_analyze_arguments(parser: argparse.ArgumentParser) -> None:
     """Add all analyze command arguments to a parser."""

src/skill_seekers/cli/arguments/pdf.py

@@ -81,6 +81,15 @@ PDF_ARGUMENTS: dict[str, dict[str, Any]] = {
             "help": "Preview workflow without executing (requires --enhance-workflow)",
         },
     },
+    # API key (parity with scrape/github/analyze)
+    "api_key": {
+        "flags": ("--api-key",),
+        "kwargs": {
+            "type": str,
+            "help": "Anthropic API key (or set ANTHROPIC_API_KEY env var)",
+            "metavar": "KEY",
+        },
+    },
     # Enhancement level
     "enhance_level": {
         "flags": ("--enhance-level",),

src/skill_seekers/cli/arguments/unified.py

@@ -72,6 +72,28 @@ UNIFIED_ARGUMENTS: dict[str, dict[str, Any]] = {
             "help": "Preview workflow stages without executing (requires --enhance-workflow)",
         },
     },
+    # API key and enhance-level (parity with scrape/github/analyze/pdf)
+    "api_key": {
+        "flags": ("--api-key",),
+        "kwargs": {
+            "type": str,
+            "help": "Anthropic API key (or set ANTHROPIC_API_KEY env var)",
+            "metavar": "KEY",
+        },
+    },
+    "enhance_level": {
+        "flags": ("--enhance-level",),
+        "kwargs": {
+            "type": int,
+            "choices": [0, 1, 2, 3],
+            "default": None,
+            "help": (
+                "Global AI enhancement level override (0=off, 1=SKILL.md, "
+                "2=+arch/config, 3=full). Overrides per-source enhance_level in config."
+            ),
+            "metavar": "LEVEL",
+        },
+    },
 }
 
 

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."

src/skill_seekers/cli/config_manager.py

@@ -58,9 +58,9 @@ class ConfigManager:
 
     def __init__(self):
         """Initialize configuration manager."""
-        self.config_dir = _get_config_dir()
-        self.config_file = self.config_dir / "config.json"
-        self.progress_dir = _get_progress_dir()
+        self.config_dir = self.CONFIG_DIR
+        self.config_file = self.CONFIG_FILE
+        self.progress_dir = self.PROGRESS_DIR
         self._ensure_directories()
 
         # Check if config file exists before loading

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()
 

src/skill_seekers/cli/unified_scraper.py

@@ -561,8 +561,9 @@ class UnifiedScraper:
             extract_docs = source.get("extract_docs", True)
             # Note: Signal flow analysis is automatic for Godot projects (C3.10)
 
-            # AI enhancement settings
-            enhance_level = source.get("enhance_level", 0)
+            # AI enhancement settings (CLI --enhance-level overrides per-source config)
+            cli_enhance_level = getattr(args, "enhance_level", None) if args is not None else None
+            enhance_level = cli_enhance_level if cli_enhance_level is not None else source.get("enhance_level", 0)
 
             # Run codebase analysis
             logger.info(f"   Analysis depth: {analysis_depth}")
@@ -972,14 +973,47 @@ class UnifiedScraper:
             self.build_skill(merged_data)
 
             # Phase 5: Enhancement Workflow Integration
-            if args is not None:
+            # Support workflow fields in JSON config as well as CLI args.
+            # JSON fields: "workflows" (list), "workflow_stages" (list), "workflow_vars" (dict)
+            # CLI args always take precedence; JSON fields are appended after.
+            json_workflows = self.config.get("workflows", [])
+            json_stages = self.config.get("workflow_stages", [])
+            json_vars = self.config.get("workflow_vars", {})
+            has_json_workflows = bool(json_workflows or json_stages or json_vars)
+
+            if args is not None or has_json_workflows:
+                import argparse
+
                 from skill_seekers.cli.workflow_runner import run_workflows
 
+                # Build effective args: use CLI args when provided, otherwise empty namespace
+                effective_args = args if args is not None else argparse.Namespace(
+                    enhance_workflow=None,
+                    enhance_stage=None,
+                    var=None,
+                    workflow_dry_run=False,
+                )
+
+                # Merge JSON workflow config into effective_args (JSON appended after CLI)
+                if json_workflows:
+                    effective_args.enhance_workflow = (
+                        list(effective_args.enhance_workflow or []) + json_workflows
+                    )
+                if json_stages:
+                    effective_args.enhance_stage = (
+                        list(effective_args.enhance_stage or []) + json_stages
+                    )
+                if json_vars:
+                    effective_args.var = (
+                        list(effective_args.var or [])
+                        + [f"{k}={v}" for k, v in json_vars.items()]
+                    )
+
                 unified_context = {
                     "name": self.config.get("name", ""),
                     "description": self.config.get("description", ""),
                 }
-                run_workflows(args, context=unified_context)
+                run_workflows(effective_args, context=unified_context)
 
             logger.info("\n" + "✅ " * 20)
             logger.info("Unified scraping complete!")
@@ -1067,6 +1101,24 @@ Examples:
         dest="workflow_dry_run",
         help="Preview workflow stages without executing (requires --enhance-workflow)",
     )
+    parser.add_argument(
+        "--api-key",
+        type=str,
+        metavar="KEY",
+        help="Anthropic API key (or set ANTHROPIC_API_KEY env var)",
+    )
+    parser.add_argument(
+        "--enhance-level",
+        type=int,
+        choices=[0, 1, 2, 3],
+        default=None,
+        metavar="LEVEL",
+        help=(
+            "Global AI enhancement level override for all sources "
+            "(0=off, 1=SKILL.md, 2=+arch/config, 3=full). "
+            "Overrides per-source enhance_level in config."
+        ),
+    )
 
     args = parser.parse_args()