Rename script interface arguments

The naming is more standard now
Fix different aspects of the documentation

Mainly:
    - Made all lines fewer than 80 columns.
    - Change strings in the documentation to reflect the actual
      filenames that these are processing (it seems that it was still
      pointing to .txt contingency tables)

Fixes #304
Add note about the interface change.
Update downstream.py to ammend interface changes

The command call to summarize_otu_by_category.py would fail because some
option names were changed.
Merge branch 'master' of git://github.com/qiime/qiime into issue_304

Conflicts:
	ChangeLog.md
Merge pull request #1252 from ElDeveloper/issue_304

Fixes issue 304