Improve heuristics and strategy for handling duplicate tool names

[markpollack]

See discussion on #4338

[colommar]

@markpollack hi!
So what is actually encouraged in the 1.1.0.M2 milestone? Maybe adding a suffix(like a AtomicInteger counting all the name while checking the list of the name) while the name is reapeated which also meets the need of the corner case(when autoconfig is down)

I'd like to have a try!

[markpollack]

sorry, I am slowly catching up on issue triage. We have this PR #4369 that should address the issue. there were several attempts at this, it unforunately isn't an easy topic to develop heuristics for.

[markpollack]

merged in #4369