What about transforming the version string into tuple (something like [this](http://stackoverflow.com/a/11887825) should do it)? It's pretty simple to compare tuples...

I don't like the idea of creating new config file, it doesn't solve similar issues in future versions. If we add version string into the config file, when there's backwards incompatible change in the future, it's enough to increase (minor) version number and users would be notified.