Automated conversion of Fortran examples for new prefix and specification array

Had to manually touch up some examples that had a second commented out problem specification set or
had comments in the middle of the equations set create start call.
Also had to manually fix the Navier-Stokes and Stokes 42Master examples that had multiple problem
specifications.
Fix example to use solver equations analytic boundary conditions

This was missed when the others were fixed previously.
Fix Python examples: ProblemSubTypes -> ProblemSubtypes
Revert changes to LargeUniAxialExtension example

Latest changes make this example fail to solve
Revert changes to cantilever example

The nightly test runs fail to solve with the last changes