Merge branch 'tisaac/feature-gentest-varsubst' into scott/test-harness-forloopfix

Multiple fixes enabling better for loop capability

Enabling args override in the shell script broke the
for loop functionality. By separating variables that
are in for loops and those that are not,

Multiple fixes enabling better for loop capability

Enabling args override in the shell script broke the
for loop functionality. By separating variables that
are in for loops and those that are not, arg override
are allowed even when for loops are present.

Because some for loops cause different outputs and
some produce the same output, we automate the two
extemes.

Also comments are now pulled out of the test specification
and placed at the top of the script.

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testparse.py: allow the original implicit loops by parsing into variables

Tests: Fix harness to parse multiple colons per line

Merge remote-tracking branch 'origin/scott/test-harness-comments'

Enable comments in test language

YAML uses # as a comment delimiter. Changes enable it.
src/sys/examples/tests/ex1.c demonstrates comment.

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with del

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with deleted sourcefile info
doc: fix manual build errors
doc: fix SOURCEH for some fortran includes that got moved
doc: fix broken manualpages - bug introduced by 1b266c9
MatMissingDiagonal() is actually not a collective operation
PetscFECreateDefault(): allow 0th order quadrature
fix gmakegentest.py to ignore *.xx files that are not source code but are in the files
increase table input size to (A->cmap->n + a->B->cmap->N) for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ()
gtest: add TEST and RM clean output for Satish
gtest: set PATH for windows DLL tests, and enable -Dpetsc_EXPORTS only during (dll) build - and not for examples
gtest: use target-specific var to deduplicate FC rules for modules
gtest: for 'allgtest' and 'allgtest-tap' - use V=0 instead of 'grep -v CC' etc..
gtest: quiet absoft compiler commands [so they can be filtered].
remove incorrect requires from more test files, remove output from -fp_trap example in test because it cannot be machine independent
gtest: windows fixes. add filter to remove filename from compiler stdout. And fix filters to use petscdiff
Removed generated requires in the wrong place from test examples.
Fix test output for additional information printed about computed eigenvalues
gtest: fix ex5f.F to use 'format' so that the output from ifort matches the one from gfortran
...

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Merge branch 'scott/testharness-update1'

When filtering test output need to send stderr also to stdout since some Fortran compilers send abort messages to stderr

removed unneeded redirect_file that was previously introduced by convertExamples.py

remove unneeded white space that was previously introduced by convertExamples.py

Updates based on team review

o report_tests.sh replaced by report_tests.py
o Example file conversion does not have spaces after comment character
per PETSc standards, and it is now parsed correctly

Introduce new test harness and script to convert from the old makefile approach to the new test harness