Basework for changes to otu_cat_sig so that you can sweep through directories, and collate or not collate the results
script can now accepted an input dir or input file, if input dir, the user has the option to collate the results into a single file, or produce a results file for every table in the passed directory. Specifying an output directory is now a required paramater to avoid confusion.
Changed @ElDeveloper's style suggestions
Added new usage example for input directory
Removed unnecessary imports at beginning of script
Updated ChangeLog.md to reflect additions to otu_category_significance for @gregcaporaso
Increased number of stochastic p-value trials.

This will reduce the chance of random test failures. Fixes #794.
Merge branch 'master' of git://github.com/qiime/qiime into otu_category_significance

Conflicts:
	ChangeLog.md
New OTUs' metadata are now handled correctly.

Fixes #796.
Modified supervised_learning to accepted an input directory, can produce individual results file or a collated results file if -w is passed
Fixing --tree_fp option type
Fixing --metric option type of cluster_quality.py
Fixing --coord_fnames and --background_color option types for compare_3d_plots.py
Fixing --conversion_type option type for convert_fastaqual_fastq.py
Adding credits
Fixing option types for demultiplex_fasta.py
Fixing --map_fname option type in denoise_wrapper.py
Fixing --output_fasta_fp option type for extract_seqs_by_sample_id.py
Updated usage examples and script description
Addressed wvwdt1 style suggestions