feat(reference-curator): Add pipeline orchestrator and refactor skill format

Pipeline Orchestrator:
- Add 07-pipeline-orchestrator skill with code/CLAUDE.md and desktop/SKILL.md
- Add /reference-curator-pipeline slash command for full workflow automation
- Add pipeline_runs and pipeline_iteration_tracker tables to schema.sql
- Add v_pipeline_status and v_pipeline_iterations views
- Add pipeline_config.yaml configuration template
- Update AGENTS.md with Reference Curator Skills section
- Update claude-project files with pipeline documentation

Skill Format Refactoring:
- Extract YAML frontmatter from SKILL.md files to separate skill.yaml
- Add tools/ directories with MCP tool documentation
- Update SKILL-FORMAT-REQUIREMENTS.md with new structure
- Add migrate-skill-structure.py script for format conversion

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

custom-skills/90-reference-curator/shared/config/pipeline_config.yaml

@@ -0,0 +1,40 @@
+# Pipeline Orchestrator Configuration
+# Copy to ~/.config/reference-curator/pipeline_config.yaml
+
+pipeline:
+  # Discovery stage
+  max_sources: 10
+
+  # Crawler stage
+  max_pages: 50
+
+  # Auto-approve settings
+  auto_approve: false
+  approval_threshold: 0.85
+
+qa_loop:
+  # Maximum iterations before escalating to manual review
+  max_refactor_iterations: 3
+  max_deep_research_iterations: 2
+  max_total_iterations: 5
+
+export:
+  # Default export format: project_files, fine_tuning, jsonl
+  default_format: project_files
+
+  # Include rejected documents in a separate folder
+  include_rejected: false
+
+state:
+  # State management backend: mysql or file
+  backend: ${STATE_BACKEND:-file}
+
+  # File-based state directory (used when backend=file)
+  state_directory: ${REFERENCE_LIBRARY_PATH:-~/reference-library}/pipeline_state/
+
+logging:
+  # Log level: DEBUG, INFO, WARNING, ERROR
+  level: INFO
+
+  # Save detailed logs for each run
+  save_run_logs: true