Remove more dead code.

These are all commented out or unused, especially variables for which there
isn't even any commented code to use them.
Normalize case of Fortran keywords.
Fix inconsistent indenting.

I hope I found everything... It seems like there was a lot of copy and
paste in the compute_* files, resulting in pretty inconsistent indents.
Fix up Par_file reading.

Remove the common blocks for the parameter file parsing. I think having
the subroutine return an error as an argument seems more Fortran-y.
Also, the calls to err_occurred in meshfem and specfem are useless as
read_value_parameters would have called stop already.

This is essentially a port of the same change from the global code.
Fix up mesher Par_file reading slightly.

This is similar to the change in the shared code. Really, we should just
replace this parser with the one in the shared code, which is more
robust. But there are the two Materials and Regions sections that are
non-standard to worry about.
Add -ggdb to recommended gfortran debug flags.

Without this flag, most backtraces are useless since there's no line
number or even function name.
Remove unnecessary allocated array.

These values are only used within the loop, so there's no need for an
array here.