Add same filter step for extensions as foundation tree

[JTFouquier]

perform filter high entropy positions and gap positions to tree prior to extending... @gregcaporaso I was under the impression that this step was important specifically for trees with excessively long branches and many sequences (i.e. necessary for foundation and not the extension trees). I can add this step later. Wondering how much work it would be to do the automated analyses that we discussed at some point. I'm happy maintaining and improving ghost-tree but the tedious-ness of these redo analyses has been extremely intense. We should discuss this further at some point. Thanks!