Work on #218, fixed git config

git config must either be global or inside a repo.
I moved the lines for initialization of git to only apply to the ghpagesclone.

update-ghpages.sh

@@ -1,9 +1,5 @@
 #!/bin/bash
 
-# Setup Git
-git config user.name "Travis-CI"
-git config user.email "travis@no.reply"
-
 # Clone gh-pages
 git clone -b gh-pages "https://${GH_REF}" ghpagesclone
 cd ghpagesclone
@@ -12,6 +8,10 @@ cd ghpagesclone
 git submodule update --init --recursive
 git submodule update --remote
 
+# Setup Git
+git config user.name "Travis-CI"
+git config user.email "travis@no.reply"
+
 # If there is a new version of the master branch
 if git status | grep patterns > /dev/null 2>&1
 then