diff --git a/vibe-check-runner.js b/vibe-check-runner.js
index f56ee94..9f7c535 100644
--- a/vibe-check-runner.js
+++ b/vibe-check-runner.js
@@ -29,8 +29,10 @@ function getModifiedFiles() {
   try {
     // In CI (daily run), check files modified in the last 24 hours.
     // We filter for non-empty lines that end in .md and are in frontend/ or backend/
-    const output = execFileSync('sh', ['-c', 'git log --since="24 hours ago" --name-only --pretty=format: | sort | uniq'], { encoding: 'utf-8' });
-    const allFiles = output.split('\n')
+    const outputLog = execFileSync('sh', ['-c', 'git log --since="24 hours ago" --name-only --pretty=format: | sort | uniq'], { encoding: 'utf-8' });
+    const outputLs = execFileSync('sh', ['-c', 'git ls-files -m -o --exclude-standard frontend backend'], { encoding: 'utf-8' });
+
+    const allFiles = [...outputLog.split('\n'), ...outputLs.split('\n')]
       .map(f => f.trim())
       .filter(f => f.length > 0)
       .filter(f => f.endsWith('.md'))
@@ -284,7 +286,7 @@ async function runVibeCheck() {
       continue;
     }
 
-    const sourceFile = project.createSourceFile(`temp_${tech}.ts`, generatedCode, { overwrite: true });
+    const sourceFile = project.createSourceFile(`temp_${tech}_${file.replace(/\//g, '_')}.ts`, generatedCode, { overwrite: true });
     const { total: score, breakdown } = analyzeAST(sourceFile, tech);
 
     console.log(`Fidelity Score for ${file}: ${score}%`);