There are a couple of small problems with debugging. Until these are fixed by JetBrains it is worth pointing them out:

libbreakgen.so

Remove this from IntelliJ-IDEA-4.5.3/bin. It is a 32 bit binary and needs to be replaced with a 64 bit one. Removing it causes no loss in functionality.

idea.lax

Add -Didea.no.launcher=true to the following line in idea.lax:

lax.nl.java.option.additional=-Xms32m -Xmx256m -Dsun.java2d.noddraw=true -Didea.system.path="~/.IntelliJIdea/system" -Didea.config.path="~/.IntelliJIdea/config" -Didea.popup.weight=heavy

Thats it. Everything then works perfectly.