I guess I found a tricky solution. It is dirty but it works natively in the eclipse debugger.
I am running in debugging mode a main method which create a thread that works as a caller. This runs the first part of the project and wait until the initialization is complete (note that the first part doesn't end here, it remains looping to show debugging information based on a static class which evolves with the second part of the program). Then it starts with an infinite loop where it just calls the second part that I want to test and change: here there are also a breakpoint. Well, now I can coding in the second parts while the eclipse debugger is waiting in the breakpoint than save it and hit F8. The debugger resumes, the algorithms runs and then it stops again in the breakpoint. Just check if works, eventually change something then save and hit F8 again without wait to re-initialize the first part of the project.
Probably this method has to be restarted after a while but still, it better then restart every time :) many thanks to all your help. If somebody has more elegant way to do that they are welcome!!