just used the CMS Made Simple 2.1.3 phar installer to upgrade from 2.0.1.1 to 2.1.3. For some reason though it tries to add dummy index.html files in all sub directories als the ones that have nothing to do with CMS Made Simple. Wouldn't it be more logical to have the installer only add these index.html files recursively starting from the default CMS Made Simple dirs:
- admin
doc
lib
modules
plugins
tmp
uploads