While trying to get both the firmware and bitstream to successfully update, I think I broke the bootloader (can't get to update mode). I tried to program the hex file in OLSv1-bootloader-v2-16MHz.zip from the thread linked to in the bootloader rescue thread, but it still doesn't go to update mode.
Pickit 3 successfully programs the chip and also verifies it ok, but I am not getting any kind of USB insertion message in dmesg and the ACT led does not get lit, even if I power up with the UPDATE button pressed down. What am I doing wrong with reflashing the bootloader?
EDIT: Are the configuration bits included in the bootloader .hex file, or do I have to set them up manually? If so that might well be my problem
note to self: configuration bits are on page 417
Ok, I managed to fix it.
For whatever reason flashing the hex from OLSv1-bootloader-v2-16MHz.zip did not leave the bootloader in a working state(wrong version, wrong configuration, ...?). I was thinking about compiling the bootloader from source so I could run it in debug mode in MPLAB to see if it is even running. In the SVN if found a bunch of dumps in /trunk/PIC-firmware-dumps/. I chose the lates 16MHz version, and it actually worked.
I am glad I didn't brick my new owls the day I received it without having a chance to really even get it to work. Also now I know how to recover the bootloader just in case I manage to break it again :)