It is 2024 now and this problem and the solution is still the same:

You have to manually add c:\ECLIPSE_WORKSPACE\PROJECT_NAME\.metadata\.plugins\org.epic.debug
as you described - and there's no way to order the individual include paths afterwards - you have to add them in the order you want them to appear...

Anyway for me, it doesn't break on breakpoints set in any package file - it only breaks at breakpoints set in the main file.

Moreover, if I set a breakpoint in a package file and another one in the main file, the debugger stops at the latter each time the breakpoint in the package file is hit - very strange.