Fixed descriptor generation for multiple root projects

This small change should fix issues #223 and #219.
Relative paths were generated using submodule baseDir, which resulted in paths like MODULE_DIR$/../ for EACH project descriptor. Now root project directory is used.

Tested it using sbt-test/sbt-idea/external-rootproject-dependency. Example:

![comparision](https://f.cloud.github.com/assets/6319267/1845227/204028c6-7579-11e3-9a89-f24c1a80d40a.png)