diff --git a/.travis.yml b/.travis.yml
index b2ebcf580..ea4a794b1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -36,10 +36,10 @@ deploy:
     branch: master
   skip_cleanup: true
   script: npm run --silent deploy -- -x -a -r https://${GH_TOKEN}@github.com/${TRAVIS_REPO_SLUG}.git
-- provider: script
-  on:
-    branch: greenkeeper/*
-  script: ./clean_greenkeeper
+# - provider: script
+#   on:
+#     branch: greenkeeper/*
+#   script: ./clean_greenkeeper
 - provider: npm
   on:
     branch:
diff --git a/clean_greenkeeper.sh b/clean_greenkeeper.sh
index 063992597..1e9e55371 100755
--- a/clean_greenkeeper.sh
+++ b/clean_greenkeeper.sh
@@ -1,19 +1,51 @@
 #!/bin/bash
-
 # gh-pages cleanup script: Switches to gh-pages branch, and removes all
 # directories that aren't listed as remote branches
 
+function deslash () {
+    # Recursively build a string of a directory's parents. E.g.,
+    # deslashed "feature/test/branch" returns feature/test feature
+    deslashed=$(dirname $1)
+    if [[ $deslashed =~ .*/.* ]]
+    then
+        echo $deslashed $(deslash $deslashed)
+    else
+        echo $deslashed
+    fi
+}
 
+# Cache current branch
 current=$(git rev-parse --abbrev-ref HEAD)
-git fetch origin
-branches=$(git branch -r --list origin/*)
-git checkout -f gh-pages
 
-# Remove all directories that aren't remote branch names
-find * -type d \( -path ./.git $(printf " -o -path ./%s" "${branches[@]//origin\//}") \) -prune -o -type d -exec rm -rfvi "$0" {} \;
+# Checkout most recent gh-pages
+git fetch upstream
+git fetch origin
+git checkout -f gh-pages-empty-history
+git reset --hard origin/gh-pages-empty-history
+
+# Make an array of directories to not delete, from the list of remote branches
+branches=$(git branch -r --list upstream/*)
+
+# Strip off the remote name prefix
+branches="${branches[@]//upstream\//}"
+
+# Add parent directories of branches to the exclusion list (e.g. greenkeeper/)
+for branch in $branches; do
+    if [[ $branch =~ .*/.* ]]; then
+        branches+=" $(deslash $branch)"
+    fi
+done
+
+# Dedupe all the greenkeepers
+branches=$(echo "${branches[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' ')
+
+# Remove all directories that don't have corresponding branches
+find . -type d \( -path ./.git $(printf " -o -path ./%s" $branches) \) -prune -o -type d -mindepth 1 -exec rm -rfv {} \;
+
+# Push
 git add -u
 git commit -m "Remove stale directories"
-git push origin
+# git push origin gh-pages
 
 # Return to where we were
 git checkout -f $current