Makefile generates different output from MPLAB X configurations

[EmbeddedMan]

Right now, when I build a bootloader using the makefile, the hex file produced does not match the hex file produced from MPLABX. I'm assuming this is because of differences in the command line options given to each system for building. I'm trying to work out the differences in command line options, but haven't hit on the magic set yet for the makefile that allows it to produce the same output as MPLAB X. I really like using the makefile as it's much faster (don't have to fire up MPLAB X) and you can have it build all hex files at one time which is awesome.

I think the task here is to harmonize the command line options between MPLAB X configurations and the makefile. I'm not saying that the MPLAB X options are exactly right - maybe they need to change too. But I think it would be good if both ways of compiling produced identical output.