DOC: Fix group_significance.py Sphinx issues

Fixes #1467 #1615.
DOC: fix remaining Sphinx errors in doc build
BUG: split_libraries_fastq.py --phred_offset no longer ignored

Fixes #1656.
Remove lanemask requirement from qiime config, store lanemask in qiime.filter

Related to #1696.
Remove qiime.quality imports

:woops:
Remove lane mask from test_ampliconnoise.py
DOC: fix capitalization
DOC: add ARB reference to qiime.filter.get_lane_mask

Based on Phil Hugenholtz's suggestion by email.
Merge pull request #1763 from jairideout/bug-fix-party

Bug fix party!