Fix some examples

[sandro-elsweijer]

Describe your changes here:
Some of the older examples did not run correctly. Fixed that.

Added help message output for example/IO/cmesh/gmsh/t8_read_msh_file.cxx and fixed some compatibility issues in example/IO/cmesh/gmsh/t8_load_and_refine_square_w_hole.cxx.

All these boxes must be checked by the reviewers before merging the pull request:

As a reviewer please read through all the code lines and make sure that the code is fully understood, bug free, well-documented and well-structured.

• The author added a BSD statement to doc/ (or already has one)

• The code compiles without warning in debugging and release mode, with and without MPI (this should be executed automatically in a github action)

  If the Pull request introduces code that is not covered by the github action (for example coupling with a new library):

  • Should this use case be added to the github action?
  • If not, does the specific use case compile and all tests pass (check manually)

• All tests pass (in various configurations, this should be executed automatically in a github action)

• New source/header files are properly added to the Makefiles

• The reviewer executed the new code features at least once and checked the results manually

• The code is covered in an existing or new test case

• New tests use the Google Test framework

• The code follows the t8code coding guidelines

• The code is well documented

• All function declarations, structs/classes and their members have a proper doxygen documentation

• All new algorithms and data structures are sufficiently optimal in terms of memory and runtime (If this should be merged, but there is still potential for optimization, create a new issue)

• Testing of this template: If you feel something is missing from this list, contact the developers