fix: update the migrate commands

examples/dynamic-variables/project.promptrek.yaml

@@ -1,4 +1,4 @@
-schema_version: 3.0.0
+schema_version: 3.1.0
 
 metadata:
   title: Dynamic Variables Example

examples/v21-plugins/autonomous-agents.promptrek.yaml

@@ -1,12 +1,11 @@
-# yaml-language-server: $schema=https://promptrek.ai/schema/v2.1.0.json
-schema_version: 2.1.0
+# yaml-language-server: $schema=https://promptrek.ai/schema/v3.1.0.json
+schema_version: 3.1.0
 metadata:
   title: Autonomous Agents Example
   description: Example agent configurations for automated tasks
   version: 1.0.0
   author: PrompTrek Team
   tags: [agents, automation, example]
-
 content: |
   # Autonomous Agents Example
 
@@ -18,114 +17,86 @@ content: |
   - **full**: Agent can act without approval
   - **partial**: Agent requires approval for sensitive operations
   - **untrusted**: Agent requires approval for all operations
+agents:
+- name: code-reviewer
+  prompt: |
+    You are an expert code reviewer with deep knowledge of software engineering
+    best practices. Your role is to:
 
-plugins:
-  agents:
-    # Code reviewer agent - reviews code automatically
-    - name: code-reviewer
-      description: Autonomous code review agent
-      system_prompt: |
-        You are an expert code reviewer with deep knowledge of software engineering
-        best practices. Your role is to:
-
-        1. Review code for quality, security, and performance issues
-        2. Suggest improvements and refactorings
-        3. Ensure code follows project conventions
-        4. Identify potential bugs and edge cases
-        5. Recommend additional tests
-
-        Be thorough but constructive in your reviews. Explain the reasoning
-        behind your suggestions.
-      tools:
-        - file_read
-        - git_diff
-        - static_analysis
-        - run_tests
-      trust_level: partial
-      requires_approval: true
-      context:
-        review_criteria: ["code_quality", "security", "performance", "testing"]
-        severity_threshold: "medium"
-      trust_metadata:
-        trusted: true
-        trust_level: partial
-        source: local
-
-    # Documentation generator agent
-    - name: doc-generator
-      description: Automatically generates and updates documentation
-      system_prompt: |
-        You are a documentation specialist. Generate clear, comprehensive
-        documentation that helps developers understand and use the code.
-
-        Focus on:
-        - Clear explanations
-        - Practical examples
-        - Common use cases
-        - API references
-        - Troubleshooting guides
-      tools:
-        - file_read
-        - file_write
-        - analyze_code_structure
-      trust_level: partial
-      requires_approval: true
+    1. Review code for quality, security, and performance issues
+    2. Suggest improvements and refactorings
+    3. Ensure code follows project conventions
+    4. Identify potential bugs and edge cases
+    5. Recommend additional tests
 
-    # Test generator agent
-    - name: test-generator
-      description: Generates unit and integration tests
-      system_prompt: |
-        You are a test automation expert. Generate comprehensive tests that:
-        - Cover normal operations
-        - Test edge cases
-        - Handle error conditions
-        - Mock external dependencies
-        - Follow testing best practices
-      tools:
-        - file_read
-        - file_write
-        - run_tests
-        - analyze_coverage
-      trust_level: partial
-      requires_approval: true
+    Be thorough but constructive in your reviews. Explain the reasoning
+    behind your suggestions.
+  description: Autonomous code review agent
+  tools: [file_read, git_diff, static_analysis, run_tests]
+  trust_level: partial
+  requires_approval: true
+  context:
+    review_criteria: [code_quality, security, performance, testing]
+    severity_threshold: medium
+  trust_metadata:
+    trusted: true
+    trust_level: partial
 
-    # Bug fixer agent - highly autonomous
-    - name: bug-fixer
-      description: Automatically fixes simple bugs
-      system_prompt: |
-        You are a bug-fixing specialist. Identify and fix bugs while:
-        - Understanding the root cause
-        - Applying minimal changes
-        - Adding tests to prevent regression
-        - Documenting the fix
-      tools:
-        - file_read
-        - file_write
-        - git_commit
-        - run_tests
-      trust_level: untrusted
-      requires_approval: true
-      context:
-        max_files_per_fix: 3
-        require_tests: true
-        auto_commit: false
+    source: local
+- name: doc-generator
+  prompt: |
+    You are a documentation specialist. Generate clear, comprehensive
+    documentation that helps developers understand and use the code.
 
-    # Refactoring agent
-    - name: refactorer
-      description: Suggests and applies code refactorings
-      system_prompt: |
-        You are a refactoring expert. Improve code quality through:
-        - Extracting functions/classes
-        - Removing duplication
-        - Simplifying complex logic
-        - Improving naming
-        - Applying design patterns
+    Focus on:
+    - Clear explanations
+    - Practical examples
+    - Common use cases
+    - API references
+    - Troubleshooting guides
+  description: Automatically generates and updates documentation
+  tools: [file_read, file_write, analyze_code_structure]
+  trust_level: partial
+  requires_approval: true
+- name: test-generator
+  prompt: |
+    You are a test automation expert. Generate comprehensive tests that:
+    - Cover normal operations
+    - Test edge cases
+    - Handle error conditions
+    - Mock external dependencies
+    - Follow testing best practices
+  description: Generates unit and integration tests
+  tools: [file_read, file_write, run_tests, analyze_coverage]
+  trust_level: partial
+  requires_approval: true
+- name: bug-fixer
+  prompt: |
+    You are a bug-fixing specialist. Identify and fix bugs while:
+    - Understanding the root cause
+    - Applying minimal changes
+    - Adding tests to prevent regression
+    - Documenting the fix
+  description: Automatically fixes simple bugs
+  tools: [file_read, file_write, git_commit, run_tests]
+  trust_level: untrusted
+  requires_approval: true
+  context:
+    max_files_per_fix: 3
+    require_tests: true
+    auto_commit: false
+- name: refactorer
+  prompt: |
+    You are a refactoring expert. Improve code quality through:
+    - Extracting functions/classes
+    - Removing duplication
+    - Simplifying complex logic
+    - Improving naming
+    - Applying design patterns
 
-        Always ensure refactorings maintain existing behavior.
-      tools:
-        - file_read
-        - file_write
-        - run_tests
-        - static_analysis
-      trust_level: untrusted
-      requires_approval: true
+    Always ensure refactorings maintain existing behavior.
+  description: Suggests and applies code refactorings
+  tools: [file_read, file_write, run_tests, static_analysis]
+  trust_level: untrusted
+  requires_approval: true
+allow_commands: false