feat: Add option to disable backup file creation in agents and CLI

README.md

@@ -151,7 +151,7 @@ The `apply` command looks for `.ruler/` in the current directory tree, reading t
 | Option                         | Description                                                                                                                                                |
 | ------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `--project-root <path>`        | Path to your project's root (default: current directory)                                                                                                   |
-| `--agents <agent1,agent2,...>` | Comma-separated list of agent names to target (amp, copilot, claude, codex, cursor, windsurf, cline, aider, firebase, gemini-cli, junie, augmentcode, kilocode) |
+| `--agents <agent1,agent2,...>` | Comma-separated list of agent names to target (amp, copilot, claude, codex, cursor, windsurf, cline, aider, firebase, gemini-cli, junie, augmentcode, kilocode, opencode, crush, goose) |
 | `--config <path>`              | Path to a custom `ruler.toml` configuration file                                                                                                           |
 | `--mcp` / `--with-mcp`         | Enable applying MCP server configurations (default: true)                                                                                                  |
 | `--no-mcp`                     | Disable applying MCP server configurations                                                                                                                 |
@@ -160,6 +160,7 @@ The `apply` command looks for `.ruler/` in the current directory tree, reading t
 | `--no-gitignore`               | Disable automatic .gitignore updates                                                                                                                       |
 | `--local-only`                 | Do not look for configuration in `$XDG_CONFIG_HOME`                                                                                                        |
 | `--verbose` / `-v`             | Display detailed output during execution                                                                                                                   |
+| `--disable-backup`             | Disable creation of `.bak` backup files when applying rules (default: false, configurable via `disable_backup` in `ruler.toml`)                        |
 
 ### Common Examples
 
@@ -199,6 +200,12 @@ ruler apply --verbose
 ruler apply --no-mcp --no-gitignore
 ```
 
+**Apply rules without creating backup files:**
+
+```bash
+ruler apply --disable-backup
+```
+
 ## Usage: The `revert` Command
 
 The `revert` command safely undoes all changes made by `ruler apply`, restoring your project to its pre-ruler state. It intelligently restores files from backups (`.bak` files) when available, or removes generated files that didn't exist before.
@@ -275,6 +282,10 @@ Defaults to `.ruler/ruler.toml` in the project root. Override with `--config` CL
 # Uses case-insensitive substring matching
 default_agents = ["copilot", "claude", "aider"]
 
+# Global backup setting - disable creation of .bak backup files 
+# (default: false, meaning backups are enabled by default)
+disable_backup = false
+
 # --- Global MCP Server Configuration ---
 [mcp]
 # Enable/disable MCP propagation globally (default: true)

src/agents/AiderAgent.ts

@@ -25,7 +25,7 @@ export class AiderAgent implements IAgent {
     const mdPath =
       agentConfig?.outputPathInstructions ??
       this.getDefaultOutputPath(projectRoot).instructions;
-    await backupFile(mdPath);
+    await backupFile(mdPath, agentConfig?.disableBackup);
     await writeGeneratedFile(mdPath, concatenatedRules);
 
     const cfgPath =
@@ -38,7 +38,7 @@ export class AiderAgent implements IAgent {
     let doc: AiderConfig = {} as AiderConfig;
     try {
       await fs.access(cfgPath);
-      await backupFile(cfgPath);
+      await backupFile(cfgPath, agentConfig?.disableBackup);
       const raw = await fs.readFile(cfgPath, 'utf8');
       doc = (yaml.load(raw) || {}) as AiderConfig;
     } catch {

src/agents/AugmentCodeAgent.ts

@@ -30,12 +30,12 @@ export class AugmentCodeAgent implements IAgent {
   ): Promise<void> {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
 
     if (rulerMcpJson) {
       const settingsPath = getVSCodeSettingsPath(projectRoot);
-      await backupFile(settingsPath);
+      await backupFile(settingsPath, agentConfig?.disableBackup);
 
       const existingSettings = await readVSCodeSettings(settingsPath);
       const augmentServers = transformRulerToAugmentMcp(rulerMcpJson);

src/agents/ClaudeAgent.ts

@@ -22,7 +22,7 @@ export class ClaudeAgent implements IAgent {
   ): Promise<void> {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/ClineAgent.ts

@@ -22,7 +22,7 @@ export class ClineAgent implements IAgent {
   ): Promise<void> {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/CodexCliAgent.ts

@@ -34,7 +34,7 @@ export class CodexCliAgent implements IAgent {
       defaults.instructions;
 
     // Write the instructions file
-    await backupFile(instructionsPath);
+    await backupFile(instructionsPath, agentConfig?.disableBackup);
     await writeGeneratedFile(instructionsPath, concatenatedRules);
 
     // Handle MCP configuration if enabled

src/agents/CopilotAgent.ts

@@ -27,7 +27,7 @@ export class CopilotAgent implements IAgent {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/CursorAgent.ts

@@ -33,7 +33,7 @@ export class CursorAgent implements IAgent {
     const content = `${frontMatter}${concatenatedRules.trimStart()}`;
 
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, content);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/FirebaseAgent.ts

@@ -22,7 +22,7 @@ export class FirebaseAgent implements IAgent {
   ): Promise<void> {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
 

src/agents/GooseAgent.ts

@@ -27,7 +27,7 @@ export class GooseAgent implements IAgent {
       this.getDefaultOutputPath(projectRoot);
 
     // Write rules to .goosehints
-    await backupFile(hintsPath);
+    await backupFile(hintsPath, agentConfig?.disableBackup);
     await writeGeneratedFile(hintsPath, concatenatedRules);
   }
 

src/agents/IAgent.ts

@@ -16,6 +16,8 @@ export interface IAgentConfig {
   outputPathConfig?: string;
   /** MCP propagation config for this agent. */
   mcp?: McpConfig;
+  /** Disable backup file creation for this agent */
+  disableBackup?: boolean;
 }
 
 export interface IAgent {

src/agents/JunieAgent.ts

@@ -27,7 +27,7 @@ export class JunieAgent implements IAgent {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/KiloCodeAgent.ts

@@ -28,7 +28,7 @@ export class KiloCodeAgent implements IAgent {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
 

src/agents/OpenCodeAgent.ts

@@ -20,7 +20,7 @@ export class OpenCodeAgent implements IAgent {
     const outputPath =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     const absolutePath = path.resolve(projectRoot, outputPath);
-    await backupFile(absolutePath);
+    await backupFile(absolutePath, agentConfig?.disableBackup);
     await writeGeneratedFile(absolutePath, concatenatedRules);
   }
 

src/agents/OpenHandsAgent.ts

@@ -22,7 +22,7 @@ export class OpenHandsAgent implements IAgent {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/agents/WindsurfAgent.ts

@@ -27,7 +27,7 @@ export class WindsurfAgent implements IAgent {
     const output =
       agentConfig?.outputPath ?? this.getDefaultOutputPath(projectRoot);
     await ensureDirExists(path.dirname(output));
-    await backupFile(output);
+    await backupFile(output, agentConfig?.disableBackup);
     await writeGeneratedFile(output, concatenatedRules);
   }
   getDefaultOutputPath(projectRoot: string): string {

src/cli/commands.ts

@@ -65,6 +65,12 @@ export function run(): void {
             'Only search for local .ruler directories, ignore global config',
           default: false,
         });
+        y.option('disable-backup', {
+          type: 'boolean',
+          description:
+            'Disable creation of backup files before applying changes',
+          default: false,
+        });
       },
       async (argv) => {
         const projectRoot = argv['project-root'] as string;
@@ -79,6 +85,13 @@ export function run(): void {
         const verbose = argv.verbose as boolean;
         const dryRun = argv['dry-run'] as boolean;
         const localOnly = argv['local-only'] as boolean;
+        // Determine backup disable preference: CLI > TOML > Default (false)
+        let backupDisablePreference: boolean | undefined;
+        if (argv['disable-backup'] !== undefined) {
+          backupDisablePreference = argv['disable-backup'] as boolean;
+        } else {
+          backupDisablePreference = undefined; // Let TOML/default decide
+        }
 
         // Determine gitignore preference: CLI > TOML > Default (enabled)
         // yargs handles --no-gitignore by setting gitignore to false
@@ -99,6 +112,7 @@ export function run(): void {
             verbose,
             dryRun,
             localOnly,
+            backupDisablePreference,
           );
           console.log('Ruler apply completed successfully.');
         } catch (err: unknown) {

src/core/ConfigLoader.ts

@@ -41,6 +41,7 @@ const rulerConfigSchema = z.object({
       enabled: z.boolean().optional(),
     })
     .optional(),
+  disable_backup: z.boolean().optional(),
 });
 
 /**
@@ -69,6 +70,8 @@ export interface LoadedConfig {
   mcp?: GlobalMcpConfig;
   /** Gitignore configuration section. */
   gitignore?: GitignoreConfig;
+  /** Global disable backup setting. */
+  disableBackup?: boolean;
 }
 
 /**
@@ -207,11 +210,16 @@ export async function loadConfig(
     gitignoreConfig.enabled = rawGitignoreSection.enabled;
   }
 
+  // Parse global disable_backup setting
+  const disableBackup =
+    typeof raw.disable_backup === 'boolean' ? raw.disable_backup : undefined;
+
   return {
     defaultAgents,
     agentConfigs,
     cliAgents,
     mcp: globalMcpConfig,
     gitignore: gitignoreConfig,
+    disableBackup,
   };
 }

src/core/FileSystemUtils.ts

@@ -94,8 +94,16 @@ export async function writeGeneratedFile(
 
 /**
  * Creates a backup of the given filePath by copying it to filePath.bak if it exists.
+ * @param filePath The file to backup
+ * @param disableBackup If true, skip creating the backup
  */
-export async function backupFile(filePath: string): Promise<void> {
+export async function backupFile(
+  filePath: string,
+  disableBackup: boolean = false,
+): Promise<void> {
+  if (disableBackup) {
+    return; // Skip backup if disabled
+  }
   try {
     await fs.access(filePath);
     await fs.copyFile(filePath, `${filePath}.bak`);

src/lib.ts

@@ -116,6 +116,7 @@ export async function applyAllAgentConfigs(
   verbose = false,
   dryRun = false,
   localOnly = false,
+  cliDisableBackup?: boolean,
 ): Promise<void> {
   // Load configuration (default_agents, per-agent overrides, CLI filters)
   logVerbose(
@@ -275,6 +276,17 @@ export async function applyAllAgentConfigs(
     );
   }
 
+  // Handle backup disable setting
+  // Configuration precedence: CLI > TOML > Default (false)
+  let disableBackup: boolean;
+  if (cliDisableBackup !== undefined) {
+    disableBackup = cliDisableBackup;
+  } else if (config.disableBackup !== undefined) {
+    disableBackup = config.disableBackup;
+  } else {
+    disableBackup = false; // Default disabled (backups enabled)
+  }
+
   // Collect all generated file paths for .gitignore
   const generatedPaths: string[] = [];
   let agentsMdWritten = false;
@@ -312,7 +324,8 @@ export async function applyAllAgentConfigs(
         }
         agentsMdWritten = true;
       }
-      let finalAgentConfig = agentConfig;
+      // Propagate disableBackup to agent config
+      let finalAgentConfig = { ...agentConfig, disableBackup };
       if (agent.getIdentifier() === 'augmentcode' && rulerMcpJson) {
         const resolvedStrategy =
           cliMcpStrategy ??
@@ -321,7 +334,7 @@ export async function applyAllAgentConfigs(
           'merge';
 
         finalAgentConfig = {
-          ...agentConfig,
+          ...finalAgentConfig,
           mcp: {
             ...agentConfig?.mcp,
             strategy: resolvedStrategy,