Logic improvements (Java 1.7+)

[lenhard]

This pull request features various improvements of the classes in the logic package with the aim to transition beyond Java 1.6 and improve quality. In particular:

• Updates license headers with current date
• Syntax optimizations: Java 1.7 use of generics (diamond operator)
• Format code according to Java conventions (C-style curly brackets, I am looking at you)
• Improves exception handling with logging
• Replace usages of Exception with more precise Exceptions
• Improves variable names
• Removes commented-out code, unused private methods (unused public methods/constructors are not eliminated)
• Use try-with-resources if possible
• Delete stale comments
• Replace StringBuffer with StringBuilder
• Remove history information from JavaDoc

(I am aware that I could push this directly, since I am now a contributor. As this started out as a pull request, I want to finish it as such. Future cotributions will be made directly to jabref/master)