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Merge pull request #43 from ColdBox/copilot/fix-claude-file-overwrite-issue
Preserve user content in agent config files on `coldbox ai refresh`
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‎models/AgentRegistry.cfc‎

Lines changed: 63 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,10 @@ component singleton {
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"gemini" : "GEMINI.md",
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"opencode" : "AGENTS.md"
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}
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AGENT_OPTIONS = [
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// Demarcation markers that wrap the ColdBox CLI-managed section
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MANAGED_SECTION_START = "<!-- COLDBOX-CLI:START -->"
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MANAGED_SECTION_END = "<!-- COLDBOX-CLI:END -->"
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AGENT_OPTIONS = [
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{
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display : "Claude (Anthropic) - Recommended for general development",
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value : "claude"
@@ -126,6 +129,61 @@ component singleton {
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// Private Helpers
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// ========================================
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/**
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* Merges newly generated managed content with any user-authored content from an existing file.
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*
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* The managed section is delimited by COLDBOX-CLI:START and COLDBOX-CLI:END HTML comment
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* markers. On refresh, only the content between those markers is replaced; everything after
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* the end marker (i.e. the user's custom documentation) is preserved unchanged.
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*
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* Behavior:
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* - File does not exist → return newContent as-is (first-time write).
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* - File exists but has no end marker → return newContent as-is (old format, no user section to preserve).
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* - File exists with end marker → replace managed section, keep user section intact.
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*
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* @filePath Absolute path to the existing agent config file (may not exist yet).
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* @newContent Freshly generated content that includes both START and END markers.
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*
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* @return Combined content with updated managed section and preserved user section.
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*/
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private string function mergeUserContent(
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required string filePath,
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required string newContent
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){
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var endMarker = static.MANAGED_SECTION_END
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// Nothing to preserve — first-time write
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if ( !fileExists( filePath ) ) {
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return newContent
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}
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var existingContent = fileRead( filePath )
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// Find the end marker in the existing file
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var endPos = findNoCase( endMarker, existingContent )
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// Old-format file (no markers) — write fresh content, no user section to preserve
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if ( !endPos ) {
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return newContent
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}
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// Extract user content: everything that comes after the end marker
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var userStartPos = endPos + len( endMarker )
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var userContent = mid( existingContent, userStartPos, len( existingContent ) - userStartPos + 1 )
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// Find the end marker position in the newly generated content
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var newEndPos = findNoCase( endMarker, newContent )
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if ( !newEndPos ) {
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// New template has no end marker — return new content plus preserved user section
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return newContent & userContent
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}
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// Slice off the managed portion of the new content (up to and including the end marker)
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var managedContent = left( newContent, newEndPos + len( endMarker ) - 1 )
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return managedContent & userContent
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}
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/**
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* Configure a single agent
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*
@@ -156,13 +214,14 @@ component singleton {
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// For Claude, write the full content to AGENTS.md and make CLAUDE.md point to it
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if ( arguments.agent == "claude" ) {
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var agentsFilePath = getDirectoryFromPath( configPath ) & "AGENTS.md"
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fileWrite( agentsFilePath, content )
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var mergedContent = mergeUserContent( agentsFilePath, content )
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fileWrite( agentsFilePath, mergedContent )
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fileWrite( configPath, "@AGENTS.md" )
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return
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}
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// Write agent config file
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fileWrite( configPath, content )
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// Write agent config file, preserving any user-authored content outside the managed section
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fileWrite( configPath, mergeUserContent( configPath, content ) )
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}
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/**

‎templates/ai/agents/agent-flat-instructions.md‎

Lines changed: 36 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,7 @@
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<!-- COLDBOX-CLI:START -->
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<!-- ⚡ This section is managed by ColdBox CLI and will be refreshed on `coldbox ai refresh`. -->
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<!-- ⚠️ Do NOT edit content between COLDBOX-CLI:START and COLDBOX-CLI:END markers — changes will be overwritten. -->
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# |PROJECT_NAME| - AI Agent Instructions
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This is a ColdBox HMVC application using the **flat template structure** where all application code lives in the webroot. Compatible with Adobe ColdFusion 2018+, Lucee 5.x+, and BoxLang 1.0+.
@@ -88,34 +92,6 @@ box testbox run
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/?fwreinit=true
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```
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## Custom Application Details
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<!-- Add project-specific information below -->
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### Business Domain
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<!-- Describe what this application does -->
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### Key Services/Models
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<!-- List important services and their responsibilities -->
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### Authentication/Security
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<!-- Describe authentication approach if applicable -->
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### API Endpoints
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<!-- Document REST API routes if applicable -->
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### Deployment
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<!-- Document deployment process -->
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### Third-Party Integrations
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<!-- List external services, APIs, or integrations -->
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## AI Integration
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This project includes AI-powered development assistance with guidelines, skills, and MCP documentation servers.
@@ -195,3 +171,35 @@ This project has access to the following Model Context Protocol (MCP) documentat
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- ColdBox Docs: https://coldbox.ortusbooks.com
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- TestBox: https://testbox.ortusbooks.com
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- WireBox: https://wirebox.ortusbooks.com
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<!-- COLDBOX-CLI:END -->
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<!-- ℹ️ YOUR PROJECT DOCUMENTATION — Add your custom details below. ColdBox CLI will NOT overwrite this section. -->
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## Custom Application Details
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<!-- Add project-specific information below -->
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### Business Domain
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<!-- Describe what this application does -->
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### Key Services/Models
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<!-- List important services and their responsibilities -->
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### Authentication/Security
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<!-- Describe authentication approach if applicable -->
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### API Endpoints
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<!-- Document REST API routes if applicable -->
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### Deployment
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<!-- Document deployment process -->
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### Third-Party Integrations
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<!-- List external services, APIs, or integrations -->

‎templates/ai/agents/agent-modern-instructions.md‎

Lines changed: 40 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,7 @@
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<!-- COLDBOX-CLI:START -->
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<!-- ⚡ This section is managed by ColdBox CLI and will be refreshed on `coldbox ai refresh`. -->
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<!-- ⚠️ Do NOT edit content between COLDBOX-CLI:START and COLDBOX-CLI:END markers — changes will be overwritten. -->
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# |PROJECT_NAME| - AI Agent Instructions
26

37
This is a ColdBox HMVC application using the **modern template structure** with application code separated from the public webroot. Compatible with Adobe ColdFusion 2018+, Lucee 5.x+, and BoxLang 1.0+.
@@ -125,38 +129,6 @@ docker-compose logs -f
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- **ORM:** |ORM_ENABLED| - Object-Relational Mapping via CBORM or Quick
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- **Migrations:** |MIGRATIONS_ENABLED| - Database version control with CommandBox Migrations
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## Custom Application Details
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<!-- Add project-specific information below -->
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### Business Domain
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<!-- Describe what this application does -->
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### Key Services/Models
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<!-- List important services and their responsibilities -->
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### Authentication/Security
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<!-- Describe authentication approach if applicable -->
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### API Endpoints
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<!-- Document REST API routes if applicable -->
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### Database
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<!-- Document database setup, migrations, seeders if applicable -->
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### Deployment
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<!-- Document deployment process -->
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### Third-Party Integrations
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<!-- List external services, APIs, or integrations -->
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## AI Integration
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This project includes AI-powered development assistance with guidelines, skills, and MCP documentation servers.
@@ -238,3 +210,39 @@ This project has access to the following Model Context Protocol (MCP) documentat
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- ColdBox Docs: https://coldbox.ortusbooks.com
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- TestBox: https://testbox.ortusbooks.com
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- WireBox: https://wirebox.ortusbooks.com
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<!-- COLDBOX-CLI:END -->
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<!-- ℹ️ YOUR PROJECT DOCUMENTATION — Add your custom details below. ColdBox CLI will NOT overwrite this section. -->
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## Custom Application Details
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<!-- Add project-specific information below -->
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### Business Domain
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<!-- Describe what this application does -->
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### Key Services/Models
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<!-- List important services and their responsibilities -->
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### Authentication/Security
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<!-- Describe authentication approach if applicable -->
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### API Endpoints
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<!-- Document REST API routes if applicable -->
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### Database
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<!-- Document database setup, migrations, seeders if applicable -->
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### Deployment
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<!-- Document deployment process -->
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### Third-Party Integrations
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<!-- List external services, APIs, or integrations -->

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