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Create/Build project. Set line breakpoint. Create/Build another project(Set it Main). Start debugger on Main project. In debugger console you'll see trying to set breakpoints on the 1-st project.
I *think* this is by design. Anyway, I'll verify that and fix it if it isn't. If it is by design (my definition of "by design" is thats how JPDA doesit) I'll close as will-not-fix (you could file an issue on debuggercore and/or debuggerjpda at that point).
Breakpoings are global in netbeans. This means all gdb breakpoints are sent to a new a new gdb session at startup. Its weird behavior, but definitely working as designed.