You can download Freescale's CodeWarrior for HCS12(X) Special Edition which is free. It has build tools and a source-level debugger. The PE Micro USB interface is supported. You can also set watchpoints, which is where the debugger monitors the value of a variable. As a special edition, there is a code size restriction, but at the cost of your time in a download and experimenting with the debugger, it might be worth a look.
There is probably a GNU version of the tools available, but I don't have any experience with those.
---Tom