diff --git a/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java b/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
index 7952fa1a049..9b69bcf660a 100644
--- a/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
+++ b/querysync/java/com/google/idea/blaze/qsync/AffectedPackagesCalculator.java
@@ -235,7 +235,7 @@ public AffectedPackages getAffectedPackages() {
 
   private boolean isIncludedInProject(Path file) {
     for (Path includePath : projectIncludes()) {
-      if (file.startsWith(includePath)) {
+      if (file.startsWith(includePath) || includePath.toString().isEmpty()) {
         for (Path excludePath : projectExcludes()) {
           if (file.startsWith(excludePath)) {
             return false;