Split up source files in groups

**Note: Do not merge**

Split up source files in three groups to make projects more friendly to use.
![tree](https://f.cloud.github.com/assets/5098411/1162494/c56b48b2-2015-11e3-8b90-eea4e336b29c.png)

If this is considered an improvement I will do a proper pull request to master.
Note that the KL25Z, LPC11U24 and LPC1347 did not have the --c99 setting for c files before, please verify if this is intended or not.