Adding square qiime image
updated usage example to match what is in qiime_test_data
Merge pull request #339 from gregcaporaso/adjust_seq_orientation

updated usage example to match what is in qiime_test_data
Updated script documentation to be a little more informative and added additional script usage example; cleaned up unnecessary backslashes.
Modified .gitignore to ignore vi .swp files.
Added two new usage examples, removed unnecessary backslashes.
cleaned up output to make it easier to cut/paste
Merge pull request #343 from gregcaporaso/script_interface_test_improvements

cleaned up output to make it easier to cut/paste
Modified usage examples for plot_taxa_summary.py to match examples in test data directory
Modified add_qiime_labels.py script to make mapping file more clear, matched up example command to test data.
Merge pull request #345 from walterst/add_qiime_labels

Modified add_qiime_labels.py script to make mapping file more clear, mat...
Changed documentation to reflect current guidelines.
Merge pull request #341 from jrrideout/vim_gitignore

Modified .gitignore to ignore vi .swp files.
Updated usage examples in merge_mapping_files.txt to match test directory files
Merge pull request #347 from lkursell/merge_mapping_files

Updated usage examples in merge_mapping_files.txt to match test director...
Merge pull request #346 from wdwvt1/tree_compare

Changed documentation to reflect current guidelines for compare_tree.py
Updated script usage examples to have better number of permutations and output dir names.
Modified for script testing
Changed usage examples to reflect actual test data files. I usage examples changed script name to %prog
Modified scripts/check_id_map.py to match the qiime test data filepaths, fixed some typos.