Merge pull request #2 from nihathrael/master

- Adds functionality to remove commented out (latex) lines.
- Does some code formatting.
Restructures directories for source code.
Adds units tests for containsReferences.
Fixes small bugs in containsReferences.
Adds testcases for removing abstract start.
Reorganizes code for abstract start removal.
Adds toyInput threshold at 10 words.
Fixes a bug that upon hitting Clear Abstract., not all error messages were cleared.
Fixes problems with bugous recogintion of multiple paragraphs.
Adds unit tests for checking of correct ending of paragraph
Several fixes on math mode recognition
Adds preference relation to display of messages.
Removes emacs files backups
Ran fixjsstyle.
Removed left-over tests.js.
Added unittests for comment removal and improved comment removal for border cases