Rule pruning algorithm is very slow

[macks22]

The RulePrunerFactory.pruneRules method is very slow. On a simple grammar inferred from a time series of length 81,200, the run time is about 5.5 minutes. I've isolated this to the routine that removes overlapping rules. The screenshot below is from a slightly refactored version of the code that pulled out the core rule pruning routines into a new class RulePruningAlgorithm. The method removeOverlappingRules corresponds to this code on master.