I downloaded the "AER" last night and took a look at it. I think it is nice and I am glad that you are sharing your efforts with us.
As far as fragmentation is concerned, I think you are fine as long as you make it clear to the users that this is a custom Arduino program as opposed to the program provided by the Arduino company. If you consider we have plug-in for Eclipse, and other IDE's, there are other branches of Arduino IDE already out there.