Remove legacy and cmake compile systems

- Remove legacy and cmake compile systems from makefiles and config
- Clean out various dead code from makefile and lib/petsc/conf/rules
- Update lib/petsc/co

Remove legacy and cmake compile systems

- Remove legacy and cmake compile systems from makefiles and config
- Clean out various dead code from makefile and lib/petsc/conf/rules
- Update lib/petsc/conf/test to build all examples, not just those beginning with ex, update examples makefiles to remove now unneeded rules
- Deprecated make gnumake, replaced with make libs

Note: retained clean-legacy since it is used by clean in rules

Commit-type: style-fix, feature
Thanks-to: Jed Brown <jed@jedbrown.org> and Satish Balay <balay@mcs.anl.gov>

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Added classname to make CreateWindowEx() work. Fixed typo in error msg

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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 haplav/feature-petscviewerview-hdf5 (pull request #1722)

add PetscViewerView_HDF5()

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

add sys_classes_viewer_tutorials-ex2%: test setting HDF5 viewer from options

doc: minor PetscViewerSetUp manpage improvement

PetscViewerView_HDF5 impl.

PetscViewerHDF5Open() now calls PetscViewerSetFromOptions().

Just like PetscViewerBinaryOpen().

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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Fixes for Matlab engine

Do not use -nojvm option, instead use -nosplash, because -nojvm caused ex31.c to crash on exit
Better -info output for starting engine
Have PetscMatlabEngineDestroy() actuall

Fixes for Matlab engine

Do not use -nojvm option, instead use -nosplash, because -nojvm caused ex31.c to crash on exit
Better -info output for starting engine
Have PetscMatlabEngineDestroy() actually call the Matlab engine function to shut down the engine

Commit-type: bug-fix, style-fix

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Add PetscBinaryBigEndian() for runtime detection of endianness

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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fix build errors with arch-linux-matlab-ilp64

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the numbe

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the number of items read
* Fix PetscViewerRead() to prevent infinite loops at EOF
* Various fixes for PetscDataType PETSC_COMPLEX

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Merged in barry/cleanup-petscstringviewer (pull request #1630)

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Merge remote-tracking branch 'origin/maint'

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Commit-type: style-fix, feature, documentation, example

Merged in abhishek/feature-log-csv (pull request #1646)

CSV print function definitions added

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

Merged in haplav/remove-petscviewerhdf5setaijnames (pull request #1644)

Get rid of PetscViewerHDF5{Get,Set}AIJNames().

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

Merged in barry/minor-getsubviewer-docs (pull request #1624)

Minor updates PetscViewerGetSubViewer(), error checking, docs

Approved-by: Václav Hapla <vaclav.hapla@erdw.ethz.ch>

Get rid of PetscViewerHDF5{Get,Set}AIJNames().

fix-issue-289

doc: no need to include petscsys.h because petscviewerhdf5.h does already

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new fi

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new file
src/vec/is/utils/hdf5io.c
- PetscViewerHDF5Load() header moved from viewerimpl.h to petscis.h
- PetscViewerHDF5ReadSizes() header moved from petscviewerhdf5.h to petscis.h

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Minor updates PetscViewerGetSubViewer(), error checking, docs

Commit-type: testing-fix, documentation

PetscViewerBinaryOpen man page: add dashes for list of options database keys