Plex: Fix orientations when extruding from a 3D boundary

Plex: Instead of forcing periodic coordinates to [0, L], it should be [lower, lower + L]

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary is periodic by a positive L[d]
- Added DMPlexGetCellCoordinates_Internal() to get localized cell
coordinates automatically, and used in plexgeometry.c
- Moved coordinate functions into dmcoordinates.c
- Moved periodicity functions into dmperiodicity.c

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Plex: Fix dimension when extruding from submesh

Plex: Fix coordinate handling in extrusion when extruding from a boundary surface

remove garbage from makefiles

Including
* unused FLAGS variables
* All: lib that did not work
* stray blank lines etc

Commit-type: housekeeping
/spend 1h

Merge branch 'haplav/plex-copy-overlap' into 'main'

DMPlexCopy_Internal: copy overlap

See merge request petsc/petsc!5200