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."""