Remove hard-coded output paths.

These should use the constant that's already defined. They also need to
be updated for the re-arranged layout.
Fix hard-coded paths in CUDA routines.

I'm not happy with this extra macro, but at least there's only one of
them instead of hard-coded paths all over the place. Ideally, the path
would be passed along from Fortran, but I'm not sure of the code flow to
be able to do that just yet.
Merge pull request #130 from QuLogic/output-paths

Remove hard-coded output paths.
added a stop statement in src/auxiliaries/smooth_vol_data.f90 and commented out all MPI statements because they break the build system; developers should use routines in src/shared/parallel.f90 only instead of calling MPI directly
Merge pull request #131 from komatits/devel

added a stop statement in src/auxiliaries/smooth_vol_data.f90 and commen...
Cleanup C code slightly.
Remove duplicate constants.h file.
Correct licence in several files.
Remove todo file after moving issues to GitHub.
Remove commented code for absorbing boundary snapshots.

It was commented out almost 3 years ago; I don't think it's going to be
reinstated any time soon.
Remove irrelevant comments.

These are just code review; not actually explaining anything.
Remove code-duplicating comments.

These comments duplicate some other code somewhere else. That's just
confusing, plus they're starting to get out of date now.
build: Remove Pyre checks.

The Pyrized version was removed in 2009, so these checks are not useful.
Fix some of the simpler warnings.
Use MPI_STATUS_IGNORE in MPI calls.

The status is not used, so this saves us an extra variable or two. As
suggested by @jedbrown in another PR for Specfem2D.
Combine duplicate get_global subroutines.

These are all the same save for one loop bound. But that nested loop can
be re-written as a single loop that works for all cases.
Combine duplicates of sort_array_coordinates.

This unfortunately causes a bit of extra allocation for unused
parameters. Hopefully I can find a workaraound for that.
Replace Numerical Routines sorting code.

Numerical Routines source code is not re-distributable in any way at all
and is 100% incompatible with the GPL.

The replacement code originates from SLATEC, which, as a product of the
US Government, is available in the public domain.
Remove unused constants.
build: Remove unnecessary cleanup.

Everything in obj/ should be in one of the variables defined in the
subdirectories. Especially when doing make clean in a subdirectory, the
entire point is to not delete all objects. Also, the realclean target
depends on the clean target, so there's no need to delete the same
things there.