feat: standardize generated files to use .Generated.cs suffix

- Update all generators (Options, Services, Enums, SubDomain) to use .Generated.cs suffix
- Update cleanup logic to only delete *.Generated.cs files
- Add transition support: cleanup also removes legacy auto-generated files by checking for <auto-generated> header
- Hand-written files in Options/Services/Extensions/Enums directories are now preserved automatically

This ensures hand-written code like AzureExtensions.cs, DockerExtensions.cs, etc.
won't be accidentally deleted when the generator runs.

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

Author: thomhurst

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/CodeGeneratorOrchestrator.cs

@@ -356,8 +356,8 @@ private static async Task WriteAssemblyInfoAsync(
 
     /// <summary>
     /// Cleans up old generated files before regenerating.
-    /// Deletes all .cs files in Options, Services, Extensions directories since they'll be regenerated.
-    /// Preserves Enums directory (only deletes .Generated.cs there) to keep manually-defined enums.
+    /// Deletes *.Generated.cs files and legacy auto-generated files (transition support).
+    /// Hand-written files (without auto-generated header) are preserved.
     /// </summary>
     private void CleanupGeneratedFiles(string outputDirectory, string toolOutputDirectory, string namespacePrefix)
     {
@@ -367,53 +367,79 @@ private void CleanupGeneratedFiles(string outputDirectory, string toolOutputDire
             return;
         }
 
-        // Directories where ALL .cs files should be deleted (completely regenerated)
-        var fullyRegeneratedDirs = new[] { "Options", "Services", "Extensions" };
+        var generatedDirs = new[] { "Options", "Services", "Extensions", "Enums" };
 
-        foreach (var subDir in fullyRegeneratedDirs)
+        foreach (var subDir in generatedDirs)
         {
             var subDirPath = Path.Combine(toolPath, subDir);
             if (!Directory.Exists(subDirPath))
             {
                 continue;
             }
 
-            // Delete ALL .cs files in this directory (they will be regenerated)
+            // Delete all *.Generated.cs files (new naming convention)
+            var generatedFiles = Directory.GetFiles(subDirPath, "*.Generated.cs", SearchOption.TopDirectoryOnly);
+            foreach (var file in generatedFiles)
+            {
+                DeleteFileIfExists(file);
+            }
+
+            // Also clean up legacy auto-generated files (transition support)
+            // These are files without .Generated.cs suffix but with <auto-generated> header
             var allCsFiles = Directory.GetFiles(subDirPath, "*.cs", SearchOption.TopDirectoryOnly);
             foreach (var file in allCsFiles)
             {
-                try
+                if (file.EndsWith(".Generated.cs", StringComparison.OrdinalIgnoreCase))
                 {
-                    File.Delete(file);
-                    _logger.LogDebug("Deleted file for regeneration: {File}", file);
+                    continue; // Already handled above
                 }
-                catch (Exception ex)
+
+                if (IsAutoGeneratedFile(file))
                 {
-                    _logger.LogWarning(ex, "Failed to delete file: {File}", file);
+                    DeleteFileIfExists(file);
                 }
             }
         }
 
-        // For Enums directory, only delete .Generated.cs files (preserve manually-defined enums)
-        var enumsPath = Path.Combine(toolPath, "Enums");
-        if (Directory.Exists(enumsPath))
+        _logger.LogInformation("Cleaned up old files in {Path}", toolPath);
+    }
+
+    /// <summary>
+    /// Checks if a file contains the auto-generated header marker.
+    /// </summary>
+    private static bool IsAutoGeneratedFile(string filePath)
+    {
+        try
         {
-            var generatedEnumFiles = Directory.GetFiles(enumsPath, "*.Generated.cs", SearchOption.TopDirectoryOnly);
-            foreach (var file in generatedEnumFiles)
+            // Read first few lines to check for auto-generated marker
+            using var reader = new StreamReader(filePath);
+            for (var i = 0; i < 5 && !reader.EndOfStream; i++)
             {
-                try
+                var line = reader.ReadLine();
+                if (line != null && line.Contains("<auto-generated>", StringComparison.OrdinalIgnoreCase))
                 {
-                    File.Delete(file);
-                    _logger.LogDebug("Deleted old generated enum file: {File}", file);
-                }
-                catch (Exception ex)
-                {
-                    _logger.LogWarning(ex, "Failed to delete old generated enum file: {File}", file);
+                    return true;
                 }
             }
+            return false;
         }
+        catch
+        {
+            return false;
+        }
+    }
 
-        _logger.LogInformation("Cleaned up old files in {Path}", toolPath);
+    private void DeleteFileIfExists(string file)
+    {
+        try
+        {
+            File.Delete(file);
+            _logger.LogDebug("Deleted old generated file: {File}", file);
+        }
+        catch (Exception ex)
+        {
+            _logger.LogWarning(ex, "Failed to delete file: {File}", file);
+        }
     }
 }
 

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/EnumGenerator.cs

@@ -15,7 +15,7 @@ public Task<IReadOnlyList<GeneratedFile>> GenerateAsync(CliToolDefinition tool,
         foreach (var enumDef in tool.AllEnums)
         {
             var content = GenerateEnum(enumDef, tool);
-            var fileName = $"{enumDef.EnumName}.cs";
+            var fileName = $"{enumDef.EnumName}.Generated.cs";
             var relativePath = Path.Combine(tool.OutputDirectory, "Enums", fileName);
 
             files.Add(new GeneratedFile

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/OptionsClassGenerator.cs

@@ -15,7 +15,7 @@ public Task<IReadOnlyList<GeneratedFile>> GenerateAsync(CliToolDefinition tool,
         foreach (var command in tool.Commands)
         {
             var content = GenerateOptionsClass(command, tool);
-            var fileName = $"{command.ClassName}.cs";
+            var fileName = $"{command.ClassName}.Generated.cs";
             var relativePath = Path.Combine(tool.OutputDirectory, "Options", fileName);
 
             files.Add(new GeneratedFile

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/ServiceImplementationGenerator.cs

@@ -15,7 +15,7 @@ public Task<IReadOnlyList<GeneratedFile>> GenerateAsync(CliToolDefinition tool,
 
         // Generate the main service implementation
         var mainContent = GenerateMainServiceClass(tool);
-        var mainFileName = $"{tool.NamespacePrefix}.cs";
+        var mainFileName = $"{tool.NamespacePrefix}.Generated.cs";
         var mainRelativePath = Path.Combine(tool.OutputDirectory, "Services", mainFileName);
 
         files.Add(new GeneratedFile

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/ServiceInterfaceGenerator.cs

@@ -11,7 +11,7 @@ public class ServiceInterfaceGenerator : ICodeGenerator
     public Task<IReadOnlyList<GeneratedFile>> GenerateAsync(CliToolDefinition tool, CancellationToken cancellationToken = default)
     {
         var content = GenerateInterface(tool);
-        var fileName = $"I{tool.NamespacePrefix}.cs";
+        var fileName = $"I{tool.NamespacePrefix}.Generated.cs";
         var relativePath = Path.Combine(tool.OutputDirectory, "Services", fileName);
 
         var files = new List<GeneratedFile>

tools/ModularPipelines.OptionsGenerator/src/ModularPipelines.OptionsGenerator/Generators/SubDomainClassGenerator.cs

@@ -94,7 +94,7 @@ private static void GenerateFilesFromTree(
             node.Depth == 0 ? parentCommand : null,
             collidingCommands.Values.ToHashSet());
 
-        var fileName = $"{node.ClassName}.cs";
+        var fileName = $"{node.ClassName}.Generated.cs";
         var relativePath = Path.Combine(tool.OutputDirectory, "Services", fileName);
 
         files.Add(new GeneratedFile