diff --git a/.gitmodules b/.gitmodules
index b548196..28c5ea9 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,27 +1,27 @@
-[submodule "pathogen"]
-	path = pathogen
+[submodule "vim/pathogen"]
+	path = vim/pathogen
 	url = https://github.com/tpope/vim-pathogen
-[submodule "bundle/molokai"]
-	path = bundle/molokai
+[submodule "vim/bundle/molokai"]
+	path = vim/bundle/molokai
 	url = https://github.com/tomasr/molokai
-[submodule "bundle/vim-markdown"]
-	path = bundle/vim-markdown
+[submodule "vim/bundle/vim-markdown"]
+	path = vim/bundle/vim-markdown
 	url = https://github.com/tpope/vim-markdown
-[submodule "bundle/vim-less"]
-	path = bundle/vim-less
+[submodule "vim/bundle/vim-less"]
+	path = vim/bundle/vim-less
 	url = https://github.com/lunaru/vim-less
-[submodule "bundle/syntastic"]
-	path = bundle/syntastic
+[submodule "vim/bundle/syntastic"]
+	path = vim/bundle/syntastic
 	url = https://github.com/scrooloose/syntastic.git
-[submodule "bundle/vim-javascript"]
-	path = bundle/vim-javascript
+[submodule "vim/bundle/vim-javascript"]
+	path = vim/bundle/vim-javascript
 	url = https://github.com/pangloss/vim-javascript
-[submodule "vim-vimlint"]
-	path = bundle/vim-vimlint
+[submodule "vim/bundle/vim-vimlint"]
+	path = vim/bundle/vim-vimlint
 	url = https://github.com/syngan/vim-vimlint
-[submodule "bundle/vim-vimlparser"]
-	path = bundle/vim-vimlparser
+[submodule "vim/bundle/vim-vimlparser"]
+	path = vim/bundle/vim-vimlparser
 	url = https://github.com/ynkdir/vim-vimlparser
-[submodule "bundle/vim-latex"]
-	path = bundle/vim-latex
+[submodule "vim/bundle/vim-latex"]
+	path = vim/bundle/vim-latex
 	url = git@github.com:lervag/vim-latex.git
diff --git a/install.sh b/install.sh
index 8414a25..12db177 100755
--- a/install.sh
+++ b/install.sh
@@ -1,28 +1,45 @@
 #!/bin/bash
 
-if [ -f $HOME/.vimrc ]
-then
-	echo "Already have a local vimrc, abort."
-	exit 1
-fi
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
-if [ ! -f $HOME/.vim/vimrc ]
-then
-	echo "Vimconfig rc not found, abort."
-	exit 2
-fi
+confirm () {
+    # call with a prompt string or use a default
+    read -r -p "${1:-Are you sure? [y/N]} " response
+    case $response in
+        [yY][eE][sS]|[yY]) 
+            true
+            ;;
+        *)
+            false
+            ;;
+    esac
+}
 
+confirmAndLink() {
+	if [ -e $2 ]
+	then
+		echo "Destination $2 already exists and will be overwritten."
+		confirm && rm -rf $2 && ln -s $1 $2
+	else
+		ln -s $1 $2
+	fi
+}
+
+cd $DIR && echo "Current working directory is ${DIR}"
 
 echo -n "Downloading dependencies... "
-cd $HOME/.vim
 
 git submodule init &> /dev/null && git submodule update &> /dev/null \
 	|| $(echo "Failed."; echo "Submodule installation failed."; exit 3)
 
-echo "Done."
+echo "done."
+
+# Install vim
+
+echo "Installing vim."
+
+confirmAndLink $DIR/vim/vimrc $HOME/.vimrc
+confirmAndLink $DIR/vim $HOME/.vim
 
-echo "Installing .vimrc"
-ln -s $HOME/.vim/vimrc $HOME/.vimrc
 
-echo
 echo "Installation finished."
diff --git a/after/ftplugin/php.vim b/vim/after/ftplugin/php.vim
similarity index 100%
rename from after/ftplugin/php.vim
rename to vim/after/ftplugin/php.vim
diff --git a/after/ftplugin/smarty.vim b/vim/after/ftplugin/smarty.vim
similarity index 100%
rename from after/ftplugin/smarty.vim
rename to vim/after/ftplugin/smarty.vim
diff --git a/autoload/pathogen.vim b/vim/autoload/pathogen.vim
similarity index 100%
rename from autoload/pathogen.vim
rename to vim/autoload/pathogen.vim
diff --git a/bundle/molokai b/vim/bundle/molokai
similarity index 100%
rename from bundle/molokai
rename to vim/bundle/molokai
diff --git a/bundle/syntastic b/vim/bundle/syntastic
similarity index 100%
rename from bundle/syntastic
rename to vim/bundle/syntastic
diff --git a/bundle/vim-javascript b/vim/bundle/vim-javascript
similarity index 100%
rename from bundle/vim-javascript
rename to vim/bundle/vim-javascript
diff --git a/bundle/vim-latex b/vim/bundle/vim-latex
similarity index 100%
rename from bundle/vim-latex
rename to vim/bundle/vim-latex
diff --git a/bundle/vim-less b/vim/bundle/vim-less
similarity index 100%
rename from bundle/vim-less
rename to vim/bundle/vim-less
diff --git a/bundle/vim-markdown b/vim/bundle/vim-markdown
similarity index 100%
rename from bundle/vim-markdown
rename to vim/bundle/vim-markdown
diff --git a/bundle/vim-vimlint b/vim/bundle/vim-vimlint
similarity index 100%
rename from bundle/vim-vimlint
rename to vim/bundle/vim-vimlint
diff --git a/bundle/vim-vimlparser b/vim/bundle/vim-vimlparser
similarity index 100%
rename from bundle/vim-vimlparser
rename to vim/bundle/vim-vimlparser
diff --git a/pathogen b/vim/pathogen
similarity index 100%
rename from pathogen
rename to vim/pathogen
diff --git a/vimrc b/vim/vimrc
similarity index 100%
rename from vimrc
rename to vim/vimrc