So I just grab the ino file compile it and it will all work......
Had 1.6.5? but things weren't working well so I uninstalled, renamed the folder to OLD and installed a brand new copy of 1.8.7.
It worked ONCE, then I did a small change to the code and expected a brand new version of the .hex file in the sketch folder but nothing was changing, the file was just the old file. Deleted the file and that was the last time the hex file was created in the sketch folder. After an hour of messing around I found the file in the old absolutely stupid directory it used to put them in.
I guess it's a bug? Don't want to bore you with all the pain trying to import the project into Studio (failed to work) or the fact that the Arduino does not want to talk to the JTAG ICE3 or the Atmel ICE.
Oh well, the last famous words, about 4 hours later.