Fixed .project files

The names should match the corresponding project name and directory name.  Fixes a bug from SVN to GIT transition.
Fixed Jenkins hash for a single element.

Since x ^ x == 0 we directly initialize c to the result of the next computation since c = 0 holds before.
Fixed bugs discovered by findbugs.

Mostly we compared two objects of different type using equals.  Additionally, some strange pieces of code were detected in the proof tracker and remove/rewritten.
Add @clause for all clauses in proof

Even for unit and empty clauses.
Merge remote-tracking branch 'christj/master'
Refactoring and Bugfixing