In the pre-built PetaLinux BSP images for 12.12 and earlier, gdbserver was included in the root filesystem.
Why is it missing in the pre-built images for 2013.04?
A change was made to the default application configuration (appconfig) for 2013.04 of PetaLinux such that inclusion of gdbserver is not automatically enabled. Thus, the pre-built images do not include gdbserver since the pre-built images use all factory defaults.
gdbserver can be added to the root filesystem by updating the appconfig and adding in gdbserver:
The gdbserver command will be located in /usr/bin of the root filesystem.