There is no way to do this at the moment. It is something that has also bothered me as well. However, there are some technical challenges to making it work that way, which is why it hasn't happened yet.
What exactly is wrong with the default start gcode and what are you trying to change it to? We've done extensive testing with our own Flashforge and it works fine.
Why are you trying to change the config file instead of editing the start gcode from within MatterControl itself? The settings in /usr/lib/MatterControl/StaticData/PrinterSettings/ are the default settings loaded when you add a new printer. Your own settings are stored in an SQLite database in ~/.local/share/MatterControl/ (in 1.6 these will be moved to .json files)
Slic3r and Cura engines are disabled for dual extrusion printers, since MatterControl currently does not support dual extrusion using those engines. I realize its a little confusing to have them completely hidden in the menu. If you want to try Slic3r anyways, switch your extruder count to 1.
Awesome - thanks unlimitedbacon - interesting in any case. But like btwebz - I don't really get what you guys have changed. Some new printers like TAZ6 etc. Wondering whether the idea of adding a optional hot end retract when doing long travels on the infill layers will be realised soon. This is something I come across every now and then. ..
It sounds like you're using CuraEngine as the slice engine, and there seems to be some flawed logic with the error message that's appearing for infill.
I'll make a bug report for it so the dev team can address it; in the meantime I suggest either switching to MatterSlice so you can use LINES as the infill type or using a lower infill density with CuraEngine.
MatterControl doesn't really work with the 5th generation Makerbots. You can export X3G files for them to print from the SD card, but you cannot connect to them directly over USB. The 5th gens use a different communications protocol than most printers, which we don't support (yet).
Nevertheless, the application should not be crashing under any circumstances. Could you run MatterControl from the terminal and post the output?
Sorry. We tried to replicate your issue using our Flashforge Creator Pro, but we were not able to do it. Maybe there is some difference between the Flashforge and the CTC that we are not aware of. Without having one here for testing, there is not much we can do.