I am not sure whether this is a bug or not. So I will ask here first.
I have developed my own hardware for a special project. For that I have copied/rewritten an own core and stored in the sketchbook / hardware folder. It works just fine. Only when I try to burn the bootloader, the IDE try to load the boorloader file from / hardware / arduino / avr / bootloader and not from / hardware / / avr / bootloader.
As a workaround I can copy the bootloader to the IDE folder.
Oh, I use the IDE version 1.5.4
Success at least.
There are different architectures support added in IDE, so you need just extra subfolder - avr.
so, everithing is the same except the bootloaders.txt file (see the same file in arduino folder and modify according that) and put this file in extra avr subfolder with own breadborad sbfolder, so now we have full path
[ArduinoProjects folder]\hardware\avr\breadboard
1.5 changes the way that add-on boards are handled in the user's Arduino directory.
It seems to be at least difficult (and perhaps impossible) to have an add-on directory structure and config files that is simultaneously compatible with 1.5 and 1.0 versions of Arduino