ex18: add test 8 testing DMPlexFindVertex

ex18: -cell_simplex no longer needed for loaded meshes

DMPlexFindVertices() impl. coordinates -> dag points lookup with tolerance.

Use L2-distance.

Resolved issues brought up in PR

Commit-type: bug-fix, style-fix
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Merged in knepley/fix-plex-hdf5-periodic (pull request #1742)

Plex+HDF5: Fix periodic output in serial

Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Merged in knepley/fix-plex-layout-submesh (pull request #1704)

Plex: Handle data layout over submeshes

Merged in knepley/feature-dualspace-bdm (pull request #1699)

Knepley/feature dualspace bdm

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Plex+HDF5: Fix periodic output in serial

fix -Wmaybe-uninitialized warnings with arch-c-exodus-dbg-builder

Plex+FE: Fixed improper reference for coordinates

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Add PetscBinaryBigEndian() for runtime detection of endianness

Plex: Handle data layout over submeshes

Merged in barry/check-bad-urls (pull request #1685)

Barry/check bad urls

Approved-by: Patrick Sanan <patrick.sanan@gmail.com>
Approved-by: Junchao Zhang <junchao.zhang@gmail.com>

PetscFE+Plex: Use cell and face geometry in boundary integration

Plex: For reference cell, use interpolated DM for coordinates

Plex ex3: Fixed format of BDM output

Plex ex3: Test now working for BDM
- Do not do interpolation tests for anything but H1 elements right now

Plex ex3: Added BDM tests

Plex ex3: Use BoxMesh to create tensor meshes

Plex ex3: Allow the user to set the constant values

Plex ex3: Allow the mesh to be a reference cell