message = "This program requires a target file to upload to the Arduino \ne.g.:sketch_feb15a.cpp\nThe extention .cpp is required, however the path may NOT be included";
title = "Path required";
:
arduinoFolder + "\\hardware\\tools\\avr\\bin\\avr-gcc -Os -Wl,--gc-sections -mmcu=" + microcontroller + " -o " + targetFolderPath + "\\" + targetFilePath + ".elf " + targetFolderPath + "\\" + targetFilePath + ".o " + targetFolderPath + "\\core.a -L" + targetFolderPath + "\\build7121856102984891376 -lm",
But that doesn't upload the .ino file; it compiles and uploads the .cpp file that the Arduino IDE has generated. I suppose that this is easier to edit than a binary, but it requires a pretty huge directory full of pre-compiled libraries to work, as well.
If you're willing to work with that quantity of pre-compiled binaries, then you might as well put the bits you are interested in changing into a separate linkable entity that is less dependent on the full Arduino environment (note that it is pretty easy to make ANY file into a "linkable entity" using avr-objcopy...)