Squashed commit of the following:

commit c95548cb941fac3b88bd53b1481d98e5d325b01a
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sun Aug 24 11:48:00 2014 -0400

    Will build projects in a background thread

commit 47b467060cf19f0b7c36b1e969783fea3285f954
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sun Aug 24 10:38:54 2014 -0400

    Fixed bug: would not enter loop to run program

commit eb02e934bff35193911155f06a4fae56ad15126a
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sat Aug 23 23:19:34 2014 -0400

    Fixed bug: would not give java program control of console when run

commit 2b06ee44fa657df6f6c3c21420b17648c0b48048
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sat Aug 23 22:19:47 2014 -0400

    Fixed bug when handling java source files that are part of a package.

commit ec8f3f5cbbe569d6e011c2dc3b479a42d31ca6e3
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sat Aug 23 21:32:39 2014 -0400

    Added testing support back in

commit 32177dc78652a3ddfa4f87636a207db44124d3e0
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sat Aug 23 21:13:21 2014 -0400

    Makes each student there own directory. (Builds only)
    Will also log the output of the build process.

commit a786b1ed9c84f7cc15dda521ca83134706d0bd22
Author: Phillip Wall <tsyshadow@gmail.com>
Date:   Sat Aug 23 19:58:10 2014 -0400

    1. Add zip file support (still needs to be tested!)
Sync with upstream
Sync with upstream
Fixed Bug: Problem with copying files with packages
Fixed Threading bugs
Fixed problem, would not exit for loop
Merge pull request #4 from DragonFire168/master

Fixed issues, successful test run