Parameter class handles parameter linking
Parameter class handles everything but javascript
Switched to using uploaded file names internally

instead of system generated ones.  Since they are uploaded using php's native function move_uploaded_file, it is safe to assume they files will be legal file names.  Plus, they will be escaped when used as command line arguments anyway.
Added parameter value escaping
Implemented directory flattening

QIIME has a habit (good or bad, you decide) of creating directories for the results it generates.  I added an additional step that flattens everything in a run directory into just one level of nested depth.  This required an additional step in file name display