Made modifications to scripts, merged library functions into single workflow file per discussion with Greg C. Should cover automation of commands for multiple input fastq files for join_paired_ends.py, extract_barcodes.py, and split_libraries_fastq.py. Putting all of these under #1715 as they are related code/functionality.
Merge branch 'all_multiple_file_command_generatorsNov132014' of github.com:walterst/qiime into all_multiple_file_command_generatorsNov132014
DOC: clarify multiple_extract_barcodes.py script docs

Also fixed bug where parameters weren't being passed to workflow.
DOC: update multiple_join_paired_ends.py script docs
ENH: add PROGRESS REPORTING :P
TST: fix failing tests introduced yesterday
DOC: update multiple_split_libraries_fastq.py script docs
DOC: update changelog to mention new batch mode scripts
Merge branch 'master' into all_multiple_file_command_generatorsNov132014

Conflicts:
	ChangeLog.md
Merge pull request #1806 from jairideout/all_multiple_file_command_generatorsNov132014

Batch mode scripts