code_healer 0.1.22 → 0.1.24

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -5,6 +5,42 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.24] - 2025-08-31
+
+### Added
+- **Aggressive File Filtering**: Implemented comprehensive filtering to prevent `tmp/`, `log/`, and other temporary files from being committed
+- **Pre-Commit Validation**: Added workspace validation before commit to ensure no temporary files slip through
+- **Mandatory MCP Usage**: Enhanced business context prompts to force Claude to use Atlassian MCP tools for Confluence/Jira integration
+- **Missing Method Fix**: Added `extract_file_path_from_error` method to resolve undefined method errors
+
+### Changed
+- **File Filtering**: Enhanced `should_skip_file?` method with aggressive patterns for temporary files at any level
+- **Git Cleanup**: Comprehensive cleanup of tracked temporary files using `git rm --cached` and `find` commands
+- **Business Context**: Changed from "optional" to "mandatory" MCP tool usage in prompts
+- **Setup Configuration**: Fixed `setup.rb` to include `mcp__atlassian` permission in command template
+
+### Fixed
+- **Temporary File Commits**: Prevents `tmp/`, `log/`, `storage/`, `coverage/` directories from being committed
+- **MCP Tool Access**: Fixed missing `mcp__atlassian` permission in setup script
+- **Syntax Error**: Removed stray `y` character that caused Ruby syntax errors
+- **Method Missing**: Added missing `extract_file_path_from_error` method to `HealingJob` class
+
+## [0.1.23] - 2025-08-27
+
+### Added
+- **Persistent Isolated Workspaces**: Implemented persistent workspaces that reuse the same isolated environment instead of cloning each time
+- **Smart Branch Checkout**: Workspaces now checkout to the configured target branch instead of cloning the current working branch
+- **Workspace Reset**: Added ability to reset workspace to clean state without deleting the entire workspace
+- **Configuration Control**: Added `persistent_workspaces` and `sticky_workspace` configuration options
+
+### Changed
+- **Workspace Strategy**: Changed from cloning new workspaces each time to reusing persistent workspaces with branch checkout
+- **Performance**: Significantly faster healing operations by avoiding repeated repository cloning
+- **Branch Targeting**: Workspaces now target the configured `pr_target_branch` instead of the current working branch
+
+### Fixed
+- **Branch Consistency**: Ensures fixes are always applied to the correct target branch regardless of current working branch
+
 ## [0.1.22] - 2025-08-27
 
 ### Fixed

data/lib/code_healer/business_context_manager.rb

@@ -181,30 +181,43 @@ module CodeHealer
         business_context = case CodeHealer::ConfigManager.business_context_strategy
         when 'confluence_only'
           "## Business Context Instructions:\n" \
-          "OPTIONAL: You can use Confluence MCP tools to enhance business context if available.\n\n" \
-          "1. If Confluence MCP is available:\n" \
+          "MANDATORY: You MUST use Confluence MCP tools to search for business context before fixing any code.\n\n" \
+          "1. **REQUIRED - Search Confluence for business context:**\n" \
           "   - Search for PRDs/specs related to '#{class_name}' / '#{method_name}'.\n" \
           "   - Query terms: '#{class_name}', '#{method_name}', 'business rules', 'validation patterns'.\n" \
-          "   - Apply any found documentation to your fix.\n\n" \
-          "2. If Confluence MCP is not available:\n" \
+          "   - Search for domain-specific business logic and requirements.\n" \
+          "   - Look for validation rules and business constraints.\n\n" \
+          "2. **After finding business context:**\n" \
+          "   - Apply ALL found business rules to your fix.\n" \
+          "   - Ensure the fix follows the documented business requirements.\n" \
+          "   - Validate that your solution aligns with business logic.\n\n" \
+          "3. **If no documentation is found:**\n" \
+          "   - Note this explicitly in your response.\n" \
           "   - Proceed with standard business logic and error handling practices.\n" \
           "   - Use common validation patterns and best practices.\n\n" \
-          "Note: MCP usage is optional - proceed with or without it."
+          "CRITICAL: You MUST search Confluence first - this is not optional!"
         when 'claude_atlassian_mcp'
           "## Business Context Instructions:\n" \
-          "OPTIONAL: You can use Atlassian MCP tools to enhance business context if available.\n\n" \
-          "1. **If Jira MCP is available:**\n" \
+          "MANDATORY: You MUST use Atlassian MCP tools to search for business context before fixing any code.\n\n" \
+          "1. **REQUIRED - Search Jira for business context:**\n" \
           "   - Search for tickets related to '#{class_name}' or '#{method_name}'\n" \
           "   - Look for bug reports, requirements, or business rules\n" \
-          "   - Apply any found ticket context to your fix\n\n" \
-          "2. **If Confluence MCP is available:**\n" \
+          "   - Search for domain-specific business logic and constraints\n" \
+          "   - Apply ALL found ticket context to your fix\n\n" \
+          "2. **REQUIRED - Search Confluence for business context:**\n" \
           "   - Search for PRDs, technical specs, or business process docs\n" \
           "   - Look for domain-specific business rules related to '#{class_name}'\n" \
-          "   - Apply any found documentation to your fix\n\n" \
-          "3. **If MCP tools are not available:**\n" \
-          "   - Proceed with standard business logic and error handling practices\n" \
-          "   - Use common validation patterns and best practices\n\n" \
-          "Note: MCP usage is optional - proceed with or without it."
+          "   - Search for validation patterns and business requirements\n" \
+          "   - Apply ALL found documentation to your fix\n\n" \
+          "3. **After finding business context:**\n" \
+          "   - Ensure your fix follows ALL documented business requirements\n" \
+          "   - Validate that your solution aligns with business logic\n" \
+          "   - Apply business rules and constraints to your solution\n\n" \
+          "4. **If no documentation is found:**\n" \
+          "   - Note this explicitly in your response.\n" \
+          "   - Proceed with standard business logic and error handling practices.\n" \
+          "   - Use common validation patterns and best practices.\n\n" \
+          "CRITICAL: You MUST search both Jira and Confluence first - this is not optional!"
         when 'jira_mcp'
           # Use Jira MCP context
           get_jira_business_context(class_name)
@@ -236,12 +249,15 @@ module CodeHealer
           
           ## Instructions:
           Please:
-          1. Analyze the error and understand the root cause
-          2. **IMPORTANT: Check if the fix requires changes to multiple files or if the root cause is in a different file**
-          3. Fix the issue considering the business rules above
-          4. Ensure the fix doesn't break other functionality
-          5. Follow Rails conventions and patterns
-          6. Make sure to write testcases for the fix
+          1. **CRITICAL: First, use Atlassian MCP tools to search for business context about '#{class_name}' and '#{method_name}'**
+          2. **REQUIRED: Search Confluence for business rules, PRDs, and validation patterns**
+          3. **REQUIRED: Search Jira for related tickets and business requirements**
+          4. Analyze the error and understand the root cause
+          5. **IMPORTANT: Check if the fix requires changes to multiple files or if the root cause is in a different file**
+          6. Fix the issue considering the business rules found in MCP tools
+          7. Ensure the fix doesn't break other functionality
+          8. Follow Rails conventions and patterns
+          9. Make sure to write testcases for the fix
           
           ## IMPORTANT: Full Codebase Access & Multi-File Fixes
           You have permission to edit ANY files in the codebase. Please:

data/lib/code_healer/claude_code_evolution_handler.rb

@@ -112,7 +112,7 @@ module CodeHealer
         escaped_prompt = prompt.gsub("'", "'\"'\"'")
     
         # Build command template for MCP tools access
-        command_template = config['command_template'] || "claude --print '{prompt}' --output-format text"
+        command_template = config['command_template'] || "claude --print '{prompt}' --output-format text --allowedTools Edit,mcp__atlassian"
     
         # Replace placeholder
         command = command_template.gsub('{prompt}', escaped_prompt)
@@ -131,7 +131,7 @@ module CodeHealer
         end
     
         # Add business context instructions
-        command += " --append-system-prompt 'Use available MCP tools for business context if needed, but proceed with the fix regardless.'"
+        command += " --append-system-prompt 'CRITICAL: Before fixing any code, you MUST use the Atlassian MCP tools to search Confluence for business context. Search for documentation about the class and method you are fixing. Only proceed with the fix after reviewing the business requirements from Confluence. If no documentation is found, note this in your response.'"
     
         # Return command
         command

data/lib/code_healer/config_manager.rb

@@ -176,9 +176,7 @@ module CodeHealer
         demo_mode? && demo_settings['skip_tests'] != false
       end
 
-      def demo_skip_pr?
-        demo_mode? && demo_settings['skip_pr'] != false
-      end
+
 
       def git_settings
         config['git'] || {}
@@ -197,6 +195,10 @@ module CodeHealer
         cfg = code_heal_directory_config
         cfg['sticky_workspace'] == true || cfg[:sticky_workspace] == true
       end
+
+      def persistent_workspaces_enabled?
+        code_heal_directory_config['persistent_workspaces'] != false
+      end
       
       def auto_cleanup_workspaces?
         code_heal_directory_config['auto_cleanup'] != false
@@ -346,7 +348,7 @@ module CodeHealer
             'timeout' => 300,
             'max_file_changes' => 10,
             'include_tests' => true,
-            'command_template' => "claude --print '{prompt}' --output-format text --permission-mode acceptEdits --allowedTools Edit",
+            'command_template' => "claude --print '{prompt}' --output-format text --permission-mode acceptEdits --allowedTools Edit,mcp__atlassian",
             'business_context_sources' => [
               'config/business_rules.yml',
               'docs/business_logic.md',
@@ -365,8 +367,7 @@ module CodeHealer
           },
           'demo' => {
             'enabled' => false,
-            'skip_tests' => true,
-            'skip_pr' => true
+            'skip_tests' => true
           },
           'git' => {
             'auto_commit' => true,
@@ -389,7 +390,9 @@ module CodeHealer
             'auto_cleanup' => true,
             'cleanup_after_hours' => 24,
             'max_workspaces' => 10,
-            'clone_strategy' => 'branch'
+            'clone_strategy' => 'branch',
+            'persistent_workspaces' => true,
+            'sticky_workspace' => false
           }
         }
       end

data/lib/code_healer/evolution_job.rb

@@ -56,13 +56,13 @@ class EvolutionJob
   def create_healing_workspace(class_name, method_name)
     puts "🏥 Creating isolated healing workspace for #{class_name}##{method_name}"
     
-    # Create unique workspace
+    # Create persistent workspace and checkout to target branch
     workspace_path = CodeHealer::HealingWorkspaceManager.create_healing_workspace(
       Rails.root.to_s,
-      nil  # Use current branch
+      CodeHealer::ConfigManager.pr_target_branch  # Use configured target branch
     )
     
-    puts "✅ Healing workspace created: #{workspace_path}"
+    puts "✅ Healing workspace ready: #{workspace_path}"
     workspace_path
   end
   

data/lib/code_healer/healing_job.rb

@@ -172,6 +172,24 @@ module CodeHealer
       puts "🔍 [HEALING_JOB] MCP tools check complete"
     end
 
+     def extract_file_path_from_error(error)
+      return nil unless error&.backtrace
+      
+      # Look for the first line that contains a file path
+      error.backtrace.each do |line|
+        if line.match?(/^(.+\.rb):\d+:in/)
+          file_path = $1
+          # Convert to absolute path if it's relative
+          if file_path.start_with?('./') || !file_path.start_with?('/')
+            file_path = File.expand_path(file_path)
+          end
+          return file_path
+        end
+      end
+      
+      nil
+    end
+    
     def parse_args(args)
       # Formats supported:
       # 1) [error_class, error_message, class_name, method_name, evolution_method, backtrace]
@@ -206,13 +224,13 @@ module CodeHealer
     def create_healing_workspace(class_name, method_name)
       puts "🏥 Creating isolated healing workspace for #{class_name}##{method_name}"
 
-      # Create unique workspace
+      # Create persistent workspace and checkout to target branch
       workspace_path = CodeHealer::HealingWorkspaceManager.create_healing_workspace(
         Rails.root.to_s,
-        nil  # Use current branch
+        CodeHealer::ConfigManager.pr_target_branch  # Use configured target branch
       )
 
-      puts "✅ Healing workspace created: #{workspace_path}"
+      puts "✅ Healing workspace ready: #{workspace_path}"
       workspace_path
     end
 

data/lib/code_healer/healing_workspace_manager.rb

@@ -8,7 +8,7 @@ module CodeHealer
       def create_healing_workspace(repo_path, branch_name = nil)
         puts "🏥 [WORKSPACE] Starting workspace creation..."
         puts "🏥 [WORKSPACE] Repo path: #{repo_path}"
-        puts "🏥 [WORKSPACE] Branch name: #{branch_name || 'current'}"
+        puts "🏥 [WORKSPACE] Target branch: #{branch_name || 'default'}"
         
         config = CodeHealer::ConfigManager.code_heal_directory_config
         puts "🏥 [WORKSPACE] Raw config: #{config.inspect}"
@@ -16,11 +16,22 @@ module CodeHealer
         base_path = config['path'] || config[:path] || '/tmp/code_healer_workspaces'
         puts "🏥 [WORKSPACE] Base heal dir: #{base_path}"
         
-        # Create unique workspace directory
-        workspace_id = "healing_#{Time.now.to_i}_#{SecureRandom.hex(4)}"
-        workspace_path = File.join(base_path, workspace_id)
+        # Use persistent workspace ID based on repo (if enabled)
+        if CodeHealer::ConfigManager.persistent_workspaces_enabled?
+          repo_name = extract_repo_name(repo_path)
+          workspace_id = "persistent_#{repo_name}"
+          workspace_path = File.join(base_path, workspace_id)
+        else
+          # Fallback to unique workspace for each healing session
+          workspace_id = "healing_#{Time.now.to_i}_#{SecureRandom.hex(4)}"
+          workspace_path = File.join(base_path, workspace_id)
+        end
         
-        puts "🏥 [WORKSPACE] Workspace ID: #{workspace_id}"
+        if CodeHealer::ConfigManager.persistent_workspaces_enabled?
+          puts "🏥 [WORKSPACE] Persistent workspace ID: #{workspace_id}"
+        else
+          puts "🏥 [WORKSPACE] Temporary workspace ID: #{workspace_id}"
+        end
         puts "🏥 [WORKSPACE] Full workspace path: #{workspace_path}"
         
         begin
@@ -29,25 +40,28 @@ module CodeHealer
           FileUtils.mkdir_p(base_path)
           puts "🏥 [WORKSPACE] Base directory created/verified: #{base_path}"
           
-          # Clone current branch to workspace
-          strategy = clone_strategy
-          puts "🏥 [WORKSPACE] Clone strategy: #{strategy}"
-          
-          if strategy == "branch"
-            puts "🏥 [WORKSPACE] Using branch-only cloning..."
-            clone_current_branch(repo_path, workspace_path, branch_name)
+          # Check if workspace already exists
+          if Dir.exist?(workspace_path) && Dir.exist?(File.join(workspace_path, '.git'))
+            if CodeHealer::ConfigManager.persistent_workspaces_enabled?
+              puts "🏥 [WORKSPACE] Persistent workspace exists, checking out to target branch..."
+              checkout_to_branch(workspace_path, branch_name, repo_path)
+            else
+              puts "🏥 [WORKSPACE] Workspace exists but persistent mode disabled, creating new one..."
+              cleanup_workspace(workspace_path, true)
+              create_persistent_workspace(repo_path, workspace_path, branch_name)
+            end
           else
-            puts "🏥 [WORKSPACE] Using full repo cloning..."
-            clone_full_repo(repo_path, workspace_path, branch_name)
+            puts "🏥 [WORKSPACE] Creating new workspace..."
+            create_persistent_workspace(repo_path, workspace_path, branch_name)
           end
           
-          puts "🏥 [WORKSPACE] Workspace creation completed successfully!"
+          puts "🏥 [WORKSPACE] Workspace ready successfully!"
           puts "🏥 [WORKSPACE] Final workspace path: #{workspace_path}"
-          puts "🏥 [WORKSPACE] Workspace contents: #{Dir.entries(workspace_path).join(', ')}"
+          puts "🏥 [WORKSPACE] Current branch: #{get_current_branch(workspace_path)}"
           workspace_path
         rescue => e
-          puts "❌ Failed to create healing workspace: #{e.message}"
-          cleanup_workspace(workspace_path) if Dir.exist?(workspace_path)
+          puts "❌ Failed to create/prepare healing workspace: #{e.message}"
+          # Don't cleanup persistent workspace on error
           raise e
         end
       end
@@ -131,6 +145,43 @@ module CodeHealer
         end
       end
       
+      def validate_workspace_for_commit(workspace_path)
+        puts "🔍 [WORKSPACE] Validating workspace for commit..."
+        
+        Dir.chdir(workspace_path) do
+          # Check for any temporary files that might have been added
+          staged_files = `git diff --cached --name-only`.strip.split("\n")
+          working_files = `git status --porcelain | grep '^ M\\|^M \\|^A ' | awk '{print $2}'`.strip.split("\n")
+          
+          all_files = (staged_files + working_files).uniq.reject(&:empty?)
+          
+          puts "🔍 [WORKSPACE] Files to be committed: #{all_files.join(', ')}"
+          
+          # Check for any temporary files
+          temp_files = all_files.select { |file| should_skip_file?(file) }
+          
+          if temp_files.any?
+            puts "⚠️ [WORKSPACE] WARNING: Temporary files detected in commit:"
+            temp_files.each { |file| puts "   - #{file}" }
+            
+            # Remove them from staging
+            temp_files.each do |file|
+              puts "🗑️ [WORKSPACE] Removing temporary file from staging: #{file}"
+              system("git reset HEAD '#{file}' 2>/dev/null || true")
+            end
+            
+            puts "🔍 [WORKSPACE] Temporary files removed from staging"
+            return false
+          end
+          
+          puts "✅ [WORKSPACE] Workspace validation passed - no temporary files detected"
+          return true
+        end
+      rescue => e
+        puts "❌ [WORKSPACE] Workspace validation failed: #{e.message}"
+        return false
+      end
+      
       def create_healing_branch(repo_path, workspace_path, branch_name)
         puts "🔄 Creating healing branch and PR from isolated workspace"
         
@@ -156,7 +207,13 @@ module CodeHealer
             system("git status --porcelain")
             
             # Add all changes (the fixes are already applied in the workspace)
-            system("git add .")
+            add_only_relevant_files(workspace_path)
+            
+            # Validate workspace before commit to ensure no temporary files
+            unless validate_workspace_for_commit(workspace_path)
+              puts "⚠️ [WORKSPACE] Workspace validation failed, retrying file addition..."
+              add_only_relevant_files(workspace_path)
+            end
             
             # Check if there are changes to commit
             if system("git diff --cached --quiet") == false
@@ -172,15 +229,18 @@ module CodeHealer
               puts "🔒 Main repository (#{repo_path}) remains completely untouched"
               puts "📝 All changes committed in isolated workspace"
               
-                          # Create pull request if auto-create is enabled and no PR was already created
-            if should_create_pull_request? && !CodeHealer::ConfigManager.demo_skip_pr?
-              puts "🔍 [WORKSPACE] Checking if PR was already created by evolution handler..."
-              # Skip PR creation if we're in a healing workflow (PR likely already created)
-              puts "🔍 [WORKSPACE] PR creation skipped - likely already created by evolution handler"
-              puts "🔍 [WORKSPACE] Review the changes and create a pull request when ready"
-            else
-              puts "🔍 [WORKSPACE] Review the changes and create a pull request when ready"
-            end
+                          # Create pull request if auto-create is enabled
+                          if should_create_pull_request?
+                            puts "🔍 [WORKSPACE] Auto-creating pull request..."
+                            pr_url = create_pull_request(healing_branch, branch_name)
+                            if pr_url
+                              puts "✅ [WORKSPACE] Pull request created: #{pr_url}"
+                            else
+                              puts "⚠️ [WORKSPACE] Failed to create pull request"
+                            end
+                          else
+                            puts "🔍 [WORKSPACE] Review the changes and create a pull request when ready"
+                          end
               
               healing_branch
             else
@@ -202,13 +262,23 @@ module CodeHealer
         end
       end
       
-      def cleanup_workspace(workspace_path)
+      def cleanup_workspace(workspace_path, force = false)
         puts "🧹 [WORKSPACE] Starting workspace cleanup..."
         puts "🧹 [WORKSPACE] Target: #{workspace_path}"
+        puts "🧹 [WORKSPACE] Force cleanup: #{force}"
         puts "🧹 [WORKSPACE] Exists: #{Dir.exist?(workspace_path)}"
         
         return unless Dir.exist?(workspace_path)
         
+        # Check if this is a persistent workspace
+        is_persistent = workspace_path.include?('persistent_')
+        
+        if is_persistent && !force
+          puts "🧹 [WORKSPACE] This is a persistent workspace - skipping cleanup"
+          puts "🧹 [WORKSPACE] Use force=true to override"
+          return
+        end
+        
         # Remove .git directory first to avoid conflicts
         git_dir = File.join(workspace_path, '.git')
         if Dir.exist?(git_dir)
@@ -258,17 +328,25 @@ module CodeHealer
         begin
           require 'octokit'
           
-          config = CodeHealer::ConfigManager.config
-          github_token = ENV['GITHUB_TOKEN']
-          repo_name = config['github_repo'] || config[:github_repo]
+          # Try to get GitHub token from environment
+          github_token = ENV['GITHUB_TOKEN'] || ENV['GITHUB_ACCESS_TOKEN']
+          
+          unless github_token
+            puts "❌ Missing GitHub token. Set GITHUB_TOKEN environment variable"
+            puts "💡 You can create a token at: https://github.com/settings/tokens"
+            return nil
+          end
+          
+          # Auto-detect repository from git remote
+          repo_name = detect_github_repository
           
-          unless github_token && repo_name
-            puts "❌ Missing GitHub token or repository configuration"
+          unless repo_name
+            puts "❌ Could not detect GitHub repository from git remote"
+            puts "💡 Make sure your repository has a GitHub remote origin"
             return nil
           end
           
-          # Parse repo name (owner/repo)
-          owner, repo = repo_name.split('/')
+          puts "🔗 Creating PR for repository: #{repo_name}"
           
           client = Octokit::Client.new(access_token: github_token)
           
@@ -283,13 +361,283 @@ module CodeHealer
             "Generated at: #{Time.now.strftime('%Y-%m-%d %H:%M:%S')}"
           )
           
+          puts "✅ Pull request created successfully: #{pr.html_url}"
           pr.html_url
         rescue => e
           puts "❌ Failed to create pull request: #{e.message}"
+          puts "💡 Check your GitHub token and repository access"
           nil
         end
       end
+
+      def detect_github_repository
+        # Try to detect from current git remote
+        Dir.chdir(Dir.pwd) do
+          remote_url = `git config --get remote.origin.url`.strip
+          
+          if remote_url.include?('github.com')
+            # Extract owner/repo from GitHub URL
+            if remote_url.include?('git@github.com:')
+              # SSH format: git@github.com:owner/repo.git
+              repo_part = remote_url.gsub('git@github.com:', '').gsub('.git', '')
+            elsif remote_url.include?('https://github.com/')
+              # HTTPS format: https://github.com/owner/repo.git
+              repo_part = remote_url.gsub('https://github.com/', '').gsub('.git', '')
+            else
+              return nil
+            end
+            puts "🔍 Detected GitHub repository: #{repo_part}"
+            return repo_part
+          end
+        end
+        
+        nil
+      rescue
+        nil
+      end
       
+      def extract_repo_name(repo_path)
+        # Extract repo name from path or git remote
+        if File.exist?(File.join(repo_path, '.git'))
+          Dir.chdir(repo_path) do
+            remote_url = `git config --get remote.origin.url`.strip
+            if remote_url.include?('/')
+              remote_url.split('/').last.gsub('.git', '')
+            else
+              File.basename(repo_path)
+            end
+          end
+        else
+          File.basename(repo_path)
+        end
+      end
+
+      def create_persistent_workspace(repo_path, workspace_path, branch_name)
+        puts "🏥 [WORKSPACE] Creating new persistent workspace..."
+        
+        # Get the GitHub remote URL
+        Dir.chdir(repo_path) do
+          remote_url = `git config --get remote.origin.url`.strip
+          if remote_url.empty?
+            puts "❌ [WORKSPACE] No remote origin found in #{repo_path}"
+            return false
+          end
+          
+          puts "🏥 [WORKSPACE] Cloning from: #{remote_url}"
+          puts "🏥 [WORKSPACE] To workspace: #{workspace_path}"
+          
+          # Clone the full repository for persistent use
+          result = system("git clone #{remote_url} #{workspace_path}")
+          if result
+            puts "🏥 [WORKSPACE] Repository cloned successfully"
+            # Now checkout to the target branch
+            checkout_to_branch(workspace_path, branch_name, repo_path)
+          else
+            puts "❌ [WORKSPACE] Failed to clone repository"
+            return false
+          end
+        end
+      end
+
+      def checkout_to_branch(workspace_path, branch_name, repo_path)
+        puts "🏥 [WORKSPACE] Checking out to target branch..."
+        
+        # Determine target branch
+        target_branch = branch_name || CodeHealer::ConfigManager.pr_target_branch || get_default_branch(repo_path)
+        puts "🏥 [WORKSPACE] Target branch: #{target_branch}"
+        
+        Dir.chdir(workspace_path) do
+          # Fetch latest changes
+          puts "🏥 [WORKSPACE] Fetching latest changes..."
+          system("git fetch origin")
+          
+          # Check if branch exists locally
+          local_branch_exists = system("git show-ref --verify --quiet refs/heads/#{target_branch}")
+          
+          if local_branch_exists
+            puts "🏥 [WORKSPACE] Checking out existing local branch: #{target_branch}"
+            system("git checkout #{target_branch}")
+          else
+            puts "🏥 [WORKSPACE] Checking out remote branch: #{target_branch}"
+            system("git checkout -b #{target_branch} origin/#{target_branch}")
+          end
+          
+          # Pull latest changes
+          puts "🏥 [WORKSPACE] Pulling latest changes..."
+          system("git pull origin #{target_branch}")
+          
+          # Ensure workspace is clean
+          puts "🏥 [WORKSPACE] Ensuring workspace is clean..."
+          system("git reset --hard HEAD")
+          system("git clean -fd")
+          
+          # Remove any tracked temporary files that shouldn't be committed - AGGRESSIVE cleanup
+          puts "🏥 [WORKSPACE] Removing tracked temporary files..."
+          
+          # Remove root level temporary directories
+          system("git rm -r --cached tmp/ 2>/dev/null || true")
+          system("git rm -r --cached log/ 2>/dev/null || true")
+          system("git rm -r --cached .bundle/ 2>/dev/null || true")
+          system("git rm -r --cached storage/ 2>/dev/null || true")
+          system("git rm -r --cached coverage/ 2>/dev/null || true")
+          system("git rm -r --cached .yardoc/ 2>/dev/null || true")
+          system("git rm -r --cached .rspec_status 2>/dev/null || true")
+          
+          # Remove any nested tmp/ or log/ directories that might be tracked
+          system("find . -name 'tmp' -type d -exec git rm -r --cached {} + 2>/dev/null || true")
+          system("find . -name 'log' -type d -exec git rm -r --cached {} + 2>/dev/null || true")
+          
+          # Remove any .tmp, .log, .cache files
+          system("find . -name '*.tmp' -exec git rm --cached {} + 2>/dev/null || true")
+          system("find . -name '*.log' -exec git rm --cached {} + 2>/dev/null || true")
+          system("find . -name '*.cache' -exec git rm --cached {} + 2>/dev/null || true")
+          
+          puts "🏥 [WORKSPACE] Successfully checked out to: #{target_branch}"
+        end
+      end
+
+      def get_default_branch(repo_path)
+        Dir.chdir(repo_path) do
+          # Try to get default branch from remote
+          default_branch = `git symbolic-ref refs/remotes/origin/HEAD 2>/dev/null`.strip
+          if default_branch.include?('origin/')
+            default_branch.gsub('refs/remotes/origin/', '')
+          else
+            # Fallback to common defaults
+            ['main', 'master'].find { |branch| system("git ls-remote --heads origin #{branch} >/dev/null 2>&1") }
+          end
+        end
+      end
+
+      def get_current_branch(workspace_path)
+        Dir.chdir(workspace_path) do
+          `git branch --show-current`.strip
+        end
+      rescue
+        'unknown'
+      end
+
+      def add_only_relevant_files(workspace_path)
+        puts "📁 [WORKSPACE] Adding only relevant files, respecting .gitignore..."
+        
+        Dir.chdir(workspace_path) do
+          # First, ensure .gitignore is respected
+          if File.exist?('.gitignore')
+            puts "📁 [WORKSPACE] Using repository's .gitignore file"
+          else
+            puts "📁 [WORKSPACE] No .gitignore found, using default patterns"
+          end
+          
+          # Get list of modified files
+          modified_files = `git status --porcelain | grep '^ M\\|^M \\|^A ' | awk '{print $2}'`.strip.split("\n")
+          
+          if modified_files.empty?
+            puts "📁 [WORKSPACE] No modified files to add"
+            return
+          end
+          
+          puts "📁 [WORKSPACE] Modified files: #{modified_files.join(', ')}"
+          
+          # Add each modified file individually
+          modified_files.each do |file|
+            next if file.empty?
+            
+            # Skip temporary and generated files
+            if should_skip_file?(file)
+              puts "📁 [WORKSPACE] Skipping temporary file: #{file}"
+              next
+            end
+            
+            puts "📁 [WORKSPACE] Adding file: #{file}"
+            system("git add '#{file}'")
+          end
+          
+          puts "📁 [WORKSPACE] File addition completed"
+        end
+      end
+
+      def should_skip_file?(file_path)
+        # Skip temporary and generated files - AGGRESSIVE filtering
+        skip_patterns = [
+          # Root level directories - NEVER commit these
+          /^tmp\//,
+          /^log\//,
+          /^\.git\//,
+          /^node_modules\//,
+          /^vendor\//,
+          /^public\/packs/,
+          /^public\/assets/,
+          /^\.bundle\//,
+          /^bootsnap/,
+          /^cache/,
+          /^storage\//,
+          /^coverage\//,
+          /^\.yardoc\//,
+          /^\.rspec_status/,
+          
+          # Any tmp/ directory at any level
+          /tmp\//,
+          
+          # Any log/ directory at any level  
+          /log\//,
+          
+          # Specific tmp subdirectories
+          /tmp\/cache\//,
+          /tmp\/bootsnap\//,
+          /tmp\/pids\//,
+          /tmp\/sockets\//,
+          /tmp\/sessions\//,
+          /tmp\/backup\//,
+          /tmp\/test\//,
+          
+          # File extensions
+          /\.tmp$/,
+          /\.log$/,
+          /\.cache$/,
+          /\.swp$/,
+          /\.swo$/,
+          /\.bak$/,
+          /\.backup$/,
+          /~$/,
+          
+          # Rails specific
+          /\.bundle\//,
+          /Gemfile\.lock\.backup/,
+          /config\/database\.yml\.backup/,
+          /config\/secrets\.yml\.backup/
+        ]
+        
+        # Additional check: if path contains 'tmp' or 'log' anywhere, skip it
+        if file_path.include?('tmp') || file_path.include?('log')
+          puts "📁 [WORKSPACE] Skipping file containing 'tmp' or 'log': #{file_path}"
+          return true
+        end
+        
+        skip_patterns.any? { |pattern| file_path.match?(pattern) }
+      end
+
+      def reset_workspace_to_clean_state(workspace_path, branch_name = nil)
+        puts "🔄 [WORKSPACE] Resetting workspace to clean state..."
+        
+        Dir.chdir(workspace_path) do
+          # Stash any uncommitted changes
+          puts "🔄 [WORKSPACE] Stashing any uncommitted changes..."
+          system("git stash")
+          
+          # Reset to clean state
+          puts "🔄 [WORKSPACE] Resetting to clean state..."
+          system("git reset --hard HEAD")
+          system("git clean -fd")
+          
+          # Checkout to target branch if specified
+          if branch_name
+            checkout_to_branch(workspace_path, branch_name, nil)
+          end
+          
+          puts "🔄 [WORKSPACE] Workspace reset to clean state"
+        end
+      end
+
       def clone_strategy
         cfg = CodeHealer::ConfigManager.code_heal_directory_config
         cfg['clone_strategy'] || cfg[:clone_strategy] || "branch"

data/lib/code_healer/setup.rb

@@ -428,7 +428,7 @@ enable_demo_mode = ask_for_yes_no("Enable demo mode for fast demonstrations?", d
 demo_config = {}
 if enable_demo_mode
   demo_config[:skip_tests] = ask_for_yes_no("Skip test generation in demo mode?", default: true)
-  demo_config[:skip_pr] = ask_for_yes_no("Skip pull request creation in demo mode?", default: true)
+
   
   puts
   puts "🚀 Demo mode will significantly speed up healing operations!"
@@ -440,7 +440,7 @@ if enable_demo_mode
   puts "   - Timeout reduced to 60 seconds for quick responses"
   puts "   - Sticky workspace enabled for faster context loading"
   puts "   - Claude session persistence for better performance"
-  puts "   - Tests and PRs skipped for immediate results"
+  puts "   - Tests skipped for immediate results (PRs still created)"
 end
 
 # Create configuration files
@@ -523,7 +523,7 @@ create_file_with_content('.env', env_content, dry_run: options[:dry_run])
         - ".git/"
         - "node_modules/"
         - "vendor/"
-      command_template: "claude --print '{prompt}' --output-format text --permission-mode acceptEdits --allowedTools Edit"
+      command_template: "claude --print '{prompt}' --output-format text --permission-mode acceptEdits --allowedTools Edit,mcp__atlassian"
       business_context_sources:
         - "config/business_rules.yml"
         - "docs/business_logic.md"
@@ -617,7 +617,6 @@ create_file_with_content('.env', env_content, dry_run: options[:dry_run])
     demo:
       enabled: #{enable_demo_mode}
       skip_tests: #{demo_config[:skip_tests] || false}
-      skip_pr: #{demo_config[:skip_pr] || false}
     
     # Performance Configuration
     performance:

data/lib/code_healer/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module CodeHealer
-  VERSION = "0.1.22"
+  VERSION = "0.1.24"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: code_healer
 version: !ruby/object:Gem::Version
-  version: 0.1.22
+  version: 0.1.24
 platform: ruby
 authors:
 - Deepan Kumar