Fixing out of order operations in mutate function

[davidkelk]

Part (all?) of the problem we are having with projects not coming from the right source is in the
mutate function. For example, 'create representation' was being called before 'create local
project' and 'mutate project'.
The purpose of this branch is to attempt to fix these issues. It has already opened up additional
problems that I have created hotfixes for.

TODO:

• Kevin, could you review the code I eventually submit? I have comments with 'DK' in them.
  Could you look at those specifically? (The 'DK' is so you can search for them in a consistent
  way.)

[kevinjalbert]

Okay sounds like a plan. Hopefully we can resolve this by Tuesday. Just make a pull request for this new branch (Branching from issue_25, then we can merge this into issue_25, which then collapses back to master).

[davidkelk]

Issues fixed so far:

• Classpath in tester.py
• Create local project was taking 'pristine' project from _SRC_DIR instead of _BACKUP_DIR (_SRC_DIR will contain a mutated project.)
• Fixed boolean in airline java program
• Fixed ant file for airline java program
• Added numerous debug output statements
• Move mutant to local project called with wrong arguments

[davidkelk]

• Fixed more bugs in create_mutant functions
• Rearranged mutation function
  After trying it out on one run it appears to work. Will look at it more Monday.

[kevinjalbert]

Sounds great! We can meet on Monday and finish this issue off (along with issue #25).

[davidkelk]

I don't think I'll be in Monday.
Git isn't accepting my push. Claims 'Everything is up to date' - when it clearly isn't. Git status shows modified files, but git commit/push on branch_27 don't work.
I give up.