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>

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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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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>

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of //faq.html since the automatic tool incorrectly replaced /faq.html to //faq.html in some locations

These are largely updates of http to https but have a variety of other website location changes

Once this branch is in master individual developers can run make checkbadURLS and fix URLs related to their projects manually

Commit-type: bug-fix, documentation

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Merged in stefano_zampini/dmplex-speedup (pull request #1665)

Last speedups to the PLEX code with large number of MPI processes

Approved-by: Matthew Knepley <knepley@gmail.com>

DMPlexPartitionLabelInvert: loop only over the neighbors

Update output files since the previous code was accessing the label values in an ordered way

DMPlexPartitionLabelInvert: added info on algorithm used

DMPLEX: speed up DMPlexPartitionLabelClosure_Private

instead of computing the closure for each point, recursively add the cone
with this optimization, using a 128^3 simplex mesh an 16 processes on m

DMPLEX: speed up DMPlexPartitionLabelClosure_Private

instead of computing the closure for each point, recursively add the cone
with this optimization, using a 128^3 simplex mesh an 16 processes on my workstation -> from 7 seconds to 1.2

Change the name of the function and its prototype since the label and ranks arguments are unused

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DMPLEX: add few missing events to help optimizing the code

Merged in dalcinl/plexpartitioner-parmetis (pull request #1648)

Reproducible ParMETIS & DMPlex repartition

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.

Merged in dalcinl/plexpartitioner-parmetis (pull request #1648)

Reproducible ParMETIS & DMPlex repartition

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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DMPLEX: remove debug view from options

fix comment

Partitioner: Prefer default type PARMETIS, then PTSCOTCH, then CHACO

PetscPartitioner: Move option for randomSeed to where it belongs

Move PtScotch internal data structure to dmpleximpl.h
Update output files

PetscPartitioner: initial vertex weights

In the case of overlapped meshes from p4est,
the assumption of cells at the end is wrong.
This at least silence the uninitialized values warning from valgrind

DMPLEX: add support to compute CSR via matrix operations

PetscPartioner: construct CSR graph only when needed

Merge remote-tracking branch 'origin/maint'

Merged in dalcinl/fix-plex-partition-squash (pull request #1619)

DMPlex: Fix repartition and overlap

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Matthew Knepley <knepley@gmail.com>

DMPlexCreatePartitionerGraph: Fix duplicate edges in distributed graphs

DMPlex: Fix DMPlexDistribute() for parallel (maybe with overlap) meshes

* Fix handling of global numbering when redistributing meshes with overlap
* Support redistribution of non-conforming meshes
*

DMPlex: Fix DMPlexDistribute() for parallel (maybe with overlap) meshes

* Fix handling of global numbering when redistributing meshes with overlap
* Support redistribution of non-conforming meshes
* Non-conforming meshes out of p4est with overlap maybe still broken

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Partitioner: Fix PARMETIS partitioner

* Add command line option to specify the random seed
* As a side effect, fix valgrind warning related to unitialized options
array being passsed to ParMETIS_V

Partitioner: Fix PARMETIS partitioner

* Add command line option to specify the random seed
* As a side effect, fix valgrind warning related to unitialized options
array being passsed to ParMETIS_V3_PartKway

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PetscPartitionerSetFromOptions: fix memory leak

Merge branch 'pr1597/florianwechsung/rebalanceflag/master' [PR #1597]

* pr1597/florianwechsung/rebalanceflag/master:
Fix: inform user about success of DMPlexRebalanceSharedPoints via a flag

Merge branch 'stefano_zampini/fix-partitioner' into maint [PR #1607]

* stefano_zampini/fix-partitioner:
small fixes to PetscPartitioner implementations