Added code to create lock files for input and output files of unpacking before performing decompressions.  This helps prevent Inbox files from getting messed up if a user tries to update their Inbox or perform other operations while their files are decompressing.
Added code to create lock files for input and output files of unpacking before performing decompressions.  This helps prevent Inbox files from getting messed up if a user tries to update their Inbox or perform other operations while their files are decompressing.

Changed all wording and variable names from "merge mate-pairs" to "paired-end join" since that seems to resonate better with the users.

Moved lock file creation for sequence stats to an earlier point because it wasn't being created before sequence stats was starting, causing some problems.

teharrison/MG-RAST,MG-RAST/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,paczian/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,paczian/MG-RAST,teharrison/MG-RAST,teharrison/MG-RAST,wilke/MG-RAST,teharrison/MG-RAST,MG-RAST/MG-RAST,MG-RAST/MG-RAST,paczian/MG-RAST,paczian/MG-RAST,wilke/MG-RAST,MG-RAST/MG-RAST,paczian/MG-RAST,MG-RAST/MG-RAST,paczian/MG-RAST,wilke/MG-RAST,wilke/MG-RAST,wilke/MG-RAST