* WIP: first version of new system of registration of data
* TODO:
 - transport
 - more testing
 - refactoring
 - fix configuration files of tests
 - fix test file
* Merge from trunk to JH-output
* WIP: new type data registration for output
* First working version of new output system
* Better debug print
* Fixed several bugs: e.g. data are really written, when it is necessary.
* First version of new output system
 - Flow can be compiled, jaj :-)
 - Transport doesn't work yet.
Added .gitignore file to repository
Merge from master.
Merge branch 'master' into JH-output
These two files (isotherm.cc and sorption.cc ) were not merged correctly in previous merge.
Removed unused method set_spacedim().
* Removed another post merge conflists and added spacedim to OutputData class.'
Copied configuration files of two tests from master branch (still some conflicts).
* WIP: New system of output data using fields

 - Only two function for registering data (one for field, second for multifiled)
 - Registered data are copied to array of double/int/nsigned int
 - Added some unit tests for testing registration of data
 - Added getter n_nodes() to mesh.h

 TODO: add much more unit tests
Add exception for xprintf error message.

- declaration of new exception
- replace call to xterminate in xprintf by throwing this exception
- add destructor of SystemInfo
Create ApplicationBase class.

- create new class
- move 'PETSC code' from Application class and system intialization to
ApplicationBase class
Use ApplicationBase class.

- add inheritance to Application class (Application is descendant of
ApplicationBase)
- implement inherited methods of Application class
- remove PETSC code from Application class
- optimization of program termination
Remove initialization and termination functions of system.
Minor improvements in build and test system.

- ignore *.orig
- *.tst rules in tests directories; to run only one con file
- commented recepie to coberture usage (cover testst)

Conflicts:
	unit_tests/system/tokenizer_test.cpp
Move parts of code from Application to ApplicationBase class.

- move calling methods of initialization and runing program.
- create auxiliary method called from constructor.
- optimization of methods what processed command arguments.
- add comments of modified methods.
More specific subtests of test 20.

covered:
- old adsorption code
- new code using tables
- new code with spatialy variable param, use non-lin solver
  directly
- all three isotherms

missing: limited solubility, concentration out of table