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When I install Truffle Debugger extension, I cannot debug regular truffle sources - stepping doesn't work. $ git clone https://github.com/graalvm/truffle $ cd truffle $ mx netbeansinit $ netbeans --open truffle/com.oracle.* and then start debugging any unit test (JavaInteropTest in my case). A breakpoint is hit, but step over just continues the execution. This isn't an environment one can work in. Disabling Truffle Debugger extension isn't enough. One needs to uninstall it.
The module was originally created for guest language users. I agree that it's an advantage to be usable also for guest language developers, thus I'll try to do something about this issue...