I just found the problem. The avrdude distributed with the digispark extras is 32bit and I have no 32 bit support installed on this computer. The micronucleus executable is 64 bit. Here is what I get when I run
find . -type f -executable -exec file '{}' \; | grep ELF
3:./tools/micronucleus: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.18, BuildID[sha1]=9fe48cd7e4a07f2d869026e2967652b69751b85c, not stripped
4:./tools/avrdude: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.24, BuildID[sha1]=4de23b7931a126b710dca8463647dd931937030c, not stripped
79:./libraries/DigiMouse/osccal.o: ELF 32-bit LSB relocatable, Atmel AVR 8-bit, version 1 (SYSV), not stripped
120:./libraries/DigiJoystick/osccal.o: ELF 32-bit LSB relocatable, Atmel AVR 8-bit, version 1 (SYSV), not stripped
239:./libraries/DigiUSB/osccal.o: ELF 32-bit LSB relocatable, Atmel AVR 8-bit, version 1 (SYSV), not stripped
244:./libraries/DigiUSB/libs-device/osccal.o: ELF 32-bit LSB relocatable, Atmel AVR 8-bit, version 1 (SYSV), not stripped
Only avrdude needs to be recompiled as a 64 bit executable. But there may be a need to offer a 32 bit version of micronucleus.