joeo here -- pesky findleaves.sh wasn't pruning directories.
diff --git a/tools/findleaves.py b/tools/findleaves.py
index 5554715..0adf188 100755
--- a/tools/findleaves.py
+++ b/tools/findleaves.py
@@ -38,7 +38,7 @@
       if check_prune:
         i = 0
         while i < len(dirs):
-          if os.path.join(root, dirs[i]) in prune:
+          if dirs[i] in prune:
             del dirs[i]
           else:
             i += 1