diff --git a/setup.sh b/setup.sh
index 389f4aeceb634a5981024491d3e2412b2d54ba52..d7c95131693e224e4e3019eb56586c4edbc88671 100644
--- a/setup.sh
+++ b/setup.sh
@@ -196,7 +196,6 @@ function manage_plugins() {
     then
         clear
         mkdir -p Plugins
-        cd Plugins
         echo "Adding/updating plugins..."
 
         for i in ${!plugins[@]}
@@ -204,7 +203,7 @@ function manage_plugins() {
             # Check if plugin is already present
             repo_name_with_extension=${plugin_repositories[$i]##*/}
             repo_name=${repo_name_with_extension%*.git}
-            path=$(git config -f ../.gitmodules --get "submodule.Plugins/${repo_name}.path")
+            path=$(git config -f .gitmodules --get "submodule.Plugins/${repo_name}.path")
             if [ $? -ne 0 ]
             then
                 plugin_present=false
@@ -218,31 +217,26 @@ function manage_plugins() {
                 then
                     # Plugin was not yet added, call git submodule add
                     echo "Add new plugin: ${plugins[$i]}"
-                    git submodule add -b ${plugin_branches[$i]} ${plugin_repositories[$i]}
+                    cd Plugins
+                    git submodule add -f -b ${plugin_branches[$i]} ${plugin_repositories[$i]}
+                    cd ..
                 else
                     # Updating existing plugin
                     echo "Update plugin: ${plugins[$i]}"
-                    cd $repo_name
+                    cd Plugins/$repo_name
                     git fetch
                     git checkout ${plugin_branches[$i]}
                     git pull
-                    cd ..
+                    cd ../..
                 fi
             else
                 if [ "$plugin_present" == true ]
                 then
                     # Remove plugin!
-                    git submodule deinit -f "$repo_name"
-                    git rm -f "$repo_name"
-
-                    git config -f ../.gitmodules --remove-section "submodule.Plugins/${repo_name}"
-                    if [ -z "$(cat ../.gitmodules)" ]; then
-                        git rm -f ../.gitmodules
-                    fi
+                    git rm -f "Plugins/$repo_name"
                 fi
             fi
         done
-        cd ..
         echo "Done, Press enter to continue."
         read x
     fi