ENH: add --negate_sample_id_fp to filter_samples_from_otu_table.py

@ebolyen and I pair-programmed this.

Fixes #1117.
DOC: update script usage examples

Based on @gregcaporaso's suggestions.
Merge pull request #1805 from jairideout/issue-1117

ENH: add --negate_sample_id_fp to filter_samples_from_otu_table.py
DOC: updated developer documentation page
DOC: fixed typo
DOC: describe reverse strand matching in reference-based OTU picking scripts

Fixes #1335.
DOC: fixes #1417
MAINT: cleaned up spacing issues
Merge pull request #1808 from gregcaporaso/little-issues

updates to script index and associated documentation
Merge pull request #1809 from jairideout/issue-1335

DOC: describe reverse strand matching in reference-based OTU picking scripts
Merge branch 'master' into all_multiple_file_command_generatorsNov132014

Conflicts:
	ChangeLog.md