diff --git a/bin/linter.mjs b/bin/linter.mjs
index bd9a976ca944..901384f8a95c 100755
--- a/bin/linter.mjs
+++ b/bin/linter.mjs
@@ -63,56 +63,79 @@ function runGit(args, options = {}) {
   });
 }
 
+/**
+ * Helper to get modified/added TypeScript files against a given git ref.
+ * Uses merge-base when possible to compare against the common ancestor (e.g. when base and branch have both moved).
+ */
+function getDiffFiles(ref) {
+  let diffTarget = ref;
+  try {
+    const mergeBase = runGit(['merge-base', ref, 'HEAD']).trim();
+    if (mergeBase) {
+      diffTarget = mergeBase;
+    }
+  } catch {
+    // If merge-base fails (e.g. shallow clone or invalid ref), fall back to using ref directly
+  }
+
+  const output = runGit([
+    'diff',
+    '--name-only',
+    '--diff-filter=ACMRT',
+    diffTarget,
+    '--',
+    '*.ts',
+  ]);
+  return output
+    .split('\n')
+    .map(f => f.trim())
+    .filter(f => f.length > 0 && existsSync(f));
+}
+
 /**
  * Returns a list of changed TypeScript files comparing against target branches/references.
  */
 function getChangedFiles() {
-  const base = process.env.GITHUB_BASE_REF || 'main';
-  const refsToTry = [
-    base,
-    `upstream/${base}`,
-    `origin/${base}`,
-    'FETCH_HEAD',
-    'HEAD~1',
-    'HEAD^',
-  ];
+  const isCI = Boolean(process.env.CI || process.env.GITHUB_ACTIONS || process.env.GITHUB_BASE_REF);
+
+  let refsToTry = [];
+  let isStrictCI = false;
+
+  if (isCI) {
+    const baseRef = process.env.GITHUB_BASE_REF;
+    if (!baseRef) {
+      throw new Error('Running in CI but GITHUB_BASE_REF environment variable is not set.');
+    }
+    refsToTry = baseRef.startsWith('origin/') ? [baseRef] : [`origin/${baseRef}`, baseRef];
+    isStrictCI = true;
+  } else {
+    let currentBranch = '';
+    try {
+      currentBranch = runGit(['rev-parse', '--abbrev-ref', 'HEAD']).trim();
+    } catch {
+      // Continue with fallback refs if branch detection fails
+    }
+
+    refsToTry = (currentBranch === 'main')
+      ? ['origin/main', 'upstream/main', 'HEAD~1']
+      : ['upstream/main', 'origin/main', 'main'];
+  }
 
   for (const ref of refsToTry) {
     try {
-      const output = runGit([
-        'diff',
-        '--name-only',
-        '--diff-filter=ACMRT',
-        ref,
-        '--',
-        '*.ts',
-      ]);
-      return output
-        .split('\n')
-        .map(f => f.trim())
-        .filter(f => f.length > 0 && existsSync(f));
+      const files = getDiffFiles(ref);
+      console.log(`Comparing against base reference: ${ref}`);
+      return files;
     } catch {
-      // Continue to the next fallback ref
+      // Continue to next ref if this one fails/does not exist
     }
   }
 
-  // Fallback to checking uncommitted working tree changes against HEAD if all specific refs fail
-  try {
-    const output = runGit([
-      'diff',
-      '--name-only',
-      '--diff-filter=ACMRT',
-      'HEAD',
-      '--',
-      '*.ts',
-    ]);
-    return output
-      .split('\n')
-      .map(f => f.trim())
-      .filter(f => f.length > 0 && existsSync(f));
-  } catch {
-    return [];
+  if (isStrictCI) {
+    throw new Error(`Failed to determine changed files against GITHUB_BASE_REF '${refsToTry[0]}' in CI.`);
   }
+
+  throw new Error(`Failed to determine changed files. Tried refs: ${refsToTry.join(', ')}`);
 }
 
 // --- ESLint Checker ---