diff --git a/src/ccs.ts b/src/ccs.ts
index eb6f2d11..ff210f8f 100644
--- a/src/ccs.ts
+++ b/src/ccs.ts
@@ -228,7 +228,8 @@ async function main(): Promise<void> {
 
   // Special case: doctor command
   if (firstArg === 'doctor' || firstArg === '--doctor') {
-    await handleDoctorCommand();
+    const shouldFix = args.includes('--fix') || args.includes('-f');
+    await handleDoctorCommand(shouldFix);
     return;
   }
 
diff --git a/src/commands/doctor-command.ts b/src/commands/doctor-command.ts
index 5d5ff175..6f4c7c65 100644
--- a/src/commands/doctor-command.ts
+++ b/src/commands/doctor-command.ts
@@ -6,14 +6,20 @@
 
 /**
  * Handle doctor command
+ * @param shouldFix - If true, attempt to fix detected issues
  */
-export async function handleDoctorCommand(): Promise<void> {
+export async function handleDoctorCommand(shouldFix = false): Promise<void> {
   const DoctorModule = await import('../management/doctor');
   const Doctor = DoctorModule.default;
   const doctor = new Doctor();
 
   await doctor.runAllChecks();
 
+  // Attempt to fix issues if --fix flag provided
+  if (shouldFix) {
+    await doctor.fixIssues();
+  }
+
   // Exit with error code if unhealthy
   process.exit(doctor.isHealthy() ? 0 : 1);
 }
diff --git a/src/commands/sync-command.ts b/src/commands/sync-command.ts
index 33244096..bb2c60c0 100644
--- a/src/commands/sync-command.ts
+++ b/src/commands/sync-command.ts
@@ -31,6 +31,15 @@ export async function handleSyncCommand(): Promise<void> {
   const manager = new ClaudeSymlinkManager();
   manager.install(false);
 
+  console.log('');
+
+  // Repair shared symlinks (~/.ccs/shared/ → ~/.claude/)
+  // This fixes symlinks broken by Claude CLI's atomic writes (e.g., toggle thinking)
+  const SharedManager = (await import('../management/shared-manager')).default;
+  const sharedManager = new SharedManager();
+  sharedManager.ensureSharedDirectories();
+  console.log(colored('[OK]', 'green') + ' Shared symlinks verified');
+
   console.log('');
   console.log(colored('[OK] Sync complete!', 'green'));
   console.log('');
diff --git a/src/management/doctor.ts b/src/management/doctor.ts
index af25862a..3dfaee1b 100644
--- a/src/management/doctor.ts
+++ b/src/management/doctor.ts
@@ -955,6 +955,49 @@ class Doctor {
     );
   }
 
+  /**
+   * Fix detected issues
+   * Currently fixes: shared symlinks broken by Claude CLI's atomic writes
+   */
+  async fixIssues(): Promise<void> {
+    console.log('');
+    console.log(header('ATTEMPTING FIXES'));
+    console.log('');
+
+    let fixed = 0;
+
+    // Fix shared symlinks (settings.json broken by Claude CLI toggle thinking, etc.)
+    const sharedSettings = path.join(this.homedir, '.ccs', 'shared', 'settings.json');
+    if (fs.existsSync(sharedSettings)) {
+      try {
+        const stats = fs.lstatSync(sharedSettings);
+        if (!stats.isSymbolicLink()) {
+          const spinner = ora('Fixing shared settings.json symlink').start();
+          try {
+            // Import and use SharedManager to fix symlinks
+            const SharedManagerModule = await import('./shared-manager');
+            const SharedManager = SharedManagerModule.default;
+            const sharedManager = new SharedManager();
+            sharedManager.ensureSharedDirectories();
+            spinner.succeed(ok('Fixed') + ' Shared settings.json symlink restored');
+            fixed++;
+          } catch (err) {
+            spinner.fail(fail('Failed') + ` Could not fix: ${(err as Error).message}`);
+          }
+        }
+      } catch (_err) {
+        // Ignore stat errors
+      }
+    }
+
+    if (fixed > 0) {
+      console.log('');
+      console.log(ok(`[OK] Fixed ${fixed} issue(s)`));
+    } else {
+      console.log(info('[i] No fixable issues detected'));
+    }
+  }
+
   /**
    * Check if the health check results are healthy
    */