identify reasonable default for mask max-gap-frequency parameter

[gregcaporaso]

Improvement Description
This filter is disabled by default (max-gap-frequency=1.0), which matches the behavior in QIIME 1 (basically, perform conservation filtering, and let the phylogenetic reconstruction program deal with the gaps). We need to determine whether this is the best approach, or whether we should be doing our own filtering, and if so, what the default should be.