feat: enhancement workflow preset system with multi-target CLI

- Add YAML-based enhancement workflow presets shipped inside the package
  (default, minimal, security-focus, architecture-comprehensive, api-documentation)
- Add `skill-seekers workflows` subcommand: list, show, copy, add, remove, validate
- copy/add/remove all accept multiple names/files in one invocation with partial-failure behaviour
- `add --name` override restricted to single-file operations
- Add 5 MCP tools: list_workflows, get_workflow, create_workflow, update_workflow, delete_workflow
- Fix: create command _add_common_args() now correctly forwards each --enhance-workflow
  as a separate flag instead of passing the whole list as a single argument
- Update README: reposition as "data layer for AI systems" with AI Skills front and centre
- Update CHANGELOG, QUICK_REFERENCE, CLAUDE.md with workflow preset details
- 1,880+ tests passing

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

src/skill_seekers/workflows/__init__.py

@@ -0,0 +1 @@
+"""Bundled default enhancement workflow presets."""

src/skill_seekers/workflows/api-documentation.yaml

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+name: api-documentation
+description: Generate comprehensive API documentation from code analysis
+version: "1.0"
+applies_to:
+  - codebase_analysis
+  - github_analysis
+variables:
+  depth: comprehensive
+stages:
+  - name: base_patterns
+    type: builtin
+    target: patterns
+    enabled: true
+    uses_history: false
+  - name: api_extraction
+    type: custom
+    target: api
+    uses_history: false
+    enabled: true
+    prompt: >
+      Extract and document all public API endpoints, functions, and interfaces
+      from this codebase.
+
+      For each API element include:
+      1. Name and signature
+      2. Purpose and description
+      3. Parameters (name, type, required/optional, description)
+      4. Return value (type, description)
+      5. Exceptions that may be raised
+      6. Usage example
+
+      Output JSON with an "api_reference" array of API elements.
+  - name: usage_examples
+    type: custom
+    target: examples
+    uses_history: true
+    enabled: true
+    prompt: >
+      Based on the API reference, create practical usage examples that demonstrate
+      common integration patterns.
+
+      Create examples for:
+      1. Basic getting-started scenario
+      2. Common use case (most frequently used APIs)
+      3. Advanced integration pattern
+      4. Error handling example
+
+      Output JSON with a "usage_examples" array where each item has
+      "title", "description", and "code" fields.
+  - name: integration_guide
+    type: custom
+    target: integration
+    uses_history: true
+    enabled: true
+    prompt: >
+      Create a concise integration guide based on the API documentation and examples.
+
+      Include:
+      1. Prerequisites and installation
+      2. Authentication setup (if applicable)
+      3. Quick start in 5 minutes
+      4. Common gotchas and how to avoid them
+      5. Links to further resources
+
+      Output JSON with an "integration_guide" object.
+post_process:
+  reorder_sections: []
+  add_metadata:
+    enhanced: true
+    workflow: api-documentation
+    has_api_docs: true

src/skill_seekers/workflows/architecture-comprehensive.yaml

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+name: architecture-comprehensive
+description: Deep architectural analysis including patterns, dependencies, and design quality
+version: "1.0"
+applies_to:
+  - codebase_analysis
+  - github_analysis
+variables:
+  depth: comprehensive
+stages:
+  - name: base_patterns
+    type: builtin
+    target: patterns
+    enabled: true
+    uses_history: false
+  - name: architecture_overview
+    type: custom
+    target: architecture
+    uses_history: false
+    enabled: true
+    prompt: >
+      Analyse the architectural patterns and design decisions in this codebase.
+
+      Identify:
+      1. Overall architectural style (MVC, microservices, layered, hexagonal, etc.)
+      2. Key design patterns used and their purpose
+      3. Component boundaries and responsibilities
+      4. Data flow between components
+      5. External dependencies and integration points
+
+      Output JSON with an "architecture" object containing:
+      - "style": primary architectural style
+      - "patterns": list of design patterns detected
+      - "components": list of key components with descriptions
+      - "data_flow": description of data flow
+      - "quality_score": 1-10 rating with justification
+  - name: dependency_analysis
+    type: custom
+    target: dependencies
+    uses_history: true
+    enabled: true
+    prompt: >
+      Based on the architectural overview, analyse the dependency structure.
+
+      Identify:
+      1. Circular dependencies (red flags)
+      2. High coupling between modules
+      3. Opportunities for dependency injection
+      4. Third-party dependency risks (outdated, unmaintained)
+      5. Suggested refactoring priorities
+
+      Output JSON with a "dependency_analysis" object.
+  - name: improvement_roadmap
+    type: custom
+    target: roadmap
+    uses_history: true
+    enabled: true
+    prompt: >
+      Based on the full architectural analysis, create an improvement roadmap.
+
+      Provide:
+      1. Top 3 quick wins (low effort, high impact)
+      2. Medium-term improvements (1-3 months)
+      3. Long-term architectural goals
+      4. Technical debt prioritisation
+
+      Output JSON with a "roadmap" object containing "quick_wins", "medium_term", and "long_term" arrays.
+post_process:
+  reorder_sections: []
+  add_metadata:
+    enhanced: true
+    workflow: architecture-comprehensive
+    deep_analysis: true

src/skill_seekers/workflows/default.yaml

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+name: default
+description: Standard AI enhancement with all features enabled
+version: "1.0"
+applies_to:
+  - codebase_analysis
+  - doc_scraping
+  - github_analysis
+variables: {}
+stages:
+  - name: base_analysis
+    type: builtin
+    target: patterns
+    enabled: true
+    uses_history: false
+  - name: test_examples
+    type: builtin
+    target: examples
+    enabled: true
+    uses_history: false
+post_process:
+  reorder_sections: []
+  add_metadata:
+    enhanced: true
+    workflow: default

src/skill_seekers/workflows/minimal.yaml

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+name: minimal
+description: Lightweight enhancement - SKILL.md only, no heavy analysis
+version: "1.0"
+applies_to:
+  - codebase_analysis
+  - doc_scraping
+  - github_analysis
+variables:
+  depth: surface
+stages:
+  - name: skill_md_polish
+    type: custom
+    target: skill_md
+    uses_history: false
+    enabled: true
+    prompt: >
+      Review the following SKILL.md content and make minimal improvements:
+      - Fix obvious formatting issues
+      - Ensure the overview section is clear and concise
+      - Remove duplicate or redundant information
+
+      Return the improved content as plain text without extra commentary.
+post_process:
+  reorder_sections: []
+  add_metadata:
+    enhanced: true
+    workflow: minimal

src/skill_seekers/workflows/security-focus.yaml

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+name: security-focus
+description: "Security-focused review: vulnerabilities, auth, data handling"
+version: "1.0"
+applies_to:
+  - codebase_analysis
+  - python
+  - javascript
+  - typescript
+variables:
+  depth: comprehensive
+stages:
+  - name: base_patterns
+    type: builtin
+    target: patterns
+    enabled: true
+    uses_history: false
+  - name: vulnerabilities
+    type: custom
+    target: security
+    uses_history: false
+    enabled: true
+    prompt: >
+      Analyze this codebase for OWASP Top 10 and common security vulnerabilities.
+
+      Focus on:
+      1. Injection flaws (SQL, command, LDAP injection)
+      2. Broken authentication and session management
+      3. Sensitive data exposure (secrets in code, logging PII)
+      4. Security misconfigurations
+      5. Cross-site scripting (XSS) risks
+      6. Insecure direct object references
+
+      Output JSON with a "findings" array where each item has:
+      - "category": vulnerability category
+      - "severity": "critical" | "high" | "medium" | "low"
+      - "description": what the issue is
+      - "recommendation": how to fix it
+  - name: auth_review
+    type: custom
+    target: auth
+    uses_history: true
+    enabled: true
+    prompt: >
+      Examine authentication and authorisation patterns in this codebase.
+
+      Review:
+      1. Token handling and storage
+      2. Password hashing mechanisms
+      3. Session expiry and invalidation
+      4. Role-based access control implementation
+      5. OAuth/JWT usage correctness
+
+      Output JSON with an "auth_analysis" object containing "strengths" and "weaknesses" arrays.
+post_process:
+  reorder_sections: []
+  add_metadata:
+    enhanced: true
+    workflow: security-focus
+    security_reviewed: true