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@Tricky, do you know about it from the very start of project? if so you have experience (green, yellow, red marks under your name at forum ;) )
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You haven't seen FvM's rank, he is the highest decorated Altera lieutenant.
I think the best tool is you and that requires familiarity with tool and concepts. I wouldn't go your way to know ahead of fitter. I will design with minimum logic in between registers and pray. One design with its files and dependencies is far too much. If you are dealing with large projects contaings 100s of design module I wonder how can you design several versions just for testing. Where is Practicality, time factor, manager's mode???