refactor: Move output_dir creation to CLOptions

No need to have this clutter up the top domain level

refactor: Remove RegisterProblems_NS from global namespace

Just call the function when we go to process CL arguments

fix(mass): Don't iterate `vec_length` in qfcreation

- `vec_length` doesn't actually do anything anymore, so it should be set
to 1

refactor: Move and rename CreateMassQFunction

chore: Cleanup stray commented lines

Merge MR !74, 'jrwrigh/refactor_restart', into 'main'

Refactor continue/restart options and backend

See merge request phypid/honee!74

feat: Add HoneeLoadInitialCondition()

refactor: Remove -continue, add use_continue_file internally

refactor: -continue_filename has no default value

refactor: Remove -continue_time_filename option

feat(file): Add HoneeCheckFilenameExtension()

Merge MR !73, 'jrwrigh/destroy_ceeds', into 'main'

fix: Destroy Ceed objects due to libCEED #1702

See merge request phypid/honee!73

fix: Destroy Ceed objects due to libCEED #1702

Merge MR !72, 'jrwrigh/jit_changes', into 'main'

fix: Change QFunctions to account for libCEED#1696

See merge request phypid/honee!72

fix: Change QFunctions to account for libCEED#1696

Merge MR !71, 'jrwrigh/fix_container_destroy', into 'main'

fix(matceed): Use new context destroy function signature

See merge request phypid/honee!71

fix(matceed): Use new context destroy function signature

See petsc!7900 and !7960

Merge MR !70, 'jrwrigh/advection_bl_outflow_height', into 'main'

feat: Add `-bl_height_factor` option

See merge request phypid/honee!70

refactor: Rename advection flags to `-advection_ic_*`

style(advdif): Use switch for IC-specific flags

feat(advdif): Add bl_height_factor option

Merge MR !69, 'jrwrigh/newtonian_unit_tests', into 'main'

style: Move Newtonian unit test to bottom of file

See merge request phypid/honee!69

style: Move Newtonian unit test to bottom of file

Merge MR !68, 'jrwrigh/operatorget', into 'main'

fix: Destroy objects from CeedOperatorFieldGet*

See merge request phypid/honee!68

style: Use CeedOperatorFieldGetData