fix: scope test skip to batch-auto and preserve .ralph config

Address reviewer feedback:
- Codex P1: only skip test validation in batch-auto mode (not fix command)
- Codex P2: clean only transient .ralph files, preserve config.yaml

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: rubenmarcus

src/loop/executor.ts

@@ -489,9 +489,11 @@ export async function runLoop(options: LoopOptions): Promise<LoopResult> {
     : null;
 
   // Detect validation commands if validation is enabled
-  // In auto mode, skip test commands — only run build/lint to avoid loops on pre-existing test failures
+  // In batch-auto mode, skip test commands — only run build/lint to avoid loops on pre-existing test failures
+  // Note: fixCommand also sets auto=true but always sets fixMode, so we use that to distinguish
   const allValidationCommands = options.validate ? detectValidationCommands(options.cwd) : [];
-  const validationCommands = options.auto
+  const isBatchAuto = options.auto && !options.fixMode;
+  const validationCommands = isBatchAuto
     ? allValidationCommands.filter((cmd) => cmd.name !== 'test')
     : allValidationCommands;
 

src/loop/task-executor.ts

@@ -103,10 +103,15 @@ export async function executeTaskBatch(options: TaskExecutionOptions): Promise<T
     };
 
     try {
-      // Clean .ralph/ directory between tasks to avoid stale context
+      // Clean transient .ralph/ files between tasks to avoid stale context
+      // Preserve durable config (config.yaml) written by ralph-starter init
       const ralphDir = join(cwd, '.ralph');
       if (existsSync(ralphDir)) {
-        rmSync(ralphDir, { recursive: true, force: true });
+        const transientFiles = ['context.md', 'progress.md', 'acceptance-criteria.md', 'plan.md'];
+        for (const file of transientFiles) {
+          const fp = join(ralphDir, file);
+          if (existsSync(fp)) rmSync(fp);
+        }
       }
 
       // Notify start