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The SearchEngine should offer an option to turn off searching for inexact matches. Example: Rename default accessible method add() to addThing(). Most of the processing time is spent to search for inaccurate references to add() in the whole workspace. This is completely unnecessary, since the refactoring should not update inexact matches. If an ONLY_EXACT_MATCHES flag could be set, the search scope would be restricted to a small bunch of CUs. This would noticeably improve performance.
The problem is that there is nothing which looks more like an accurate match than an inaccurate one. This means that we still need to locate a match before we decide it is accurate vs. inaccurate. So what you suggest wouldn't make any difference. BTW, refactoring should warn if coming across inaccurate matches. Not processing them is ok, but this is likely going to cause inconsistencies.