Fix of throwing exceptions.

- change of try-chatch block in ApplicationBase::init method
- add unit test of ApplicationBase class
- remove dependance on PETSC library in source file system.cc
Program version reflects in PDF documentation.

After running "make inputref" and "make ref-doc" the reference manual contains the actual version and revision number defined in main.cc.

Fix #36.
Merge branch 'master' into JS_heat_equation