[NCF-286]/e-support:JVN-123940

using cygwin64 causes a couple of bugs during make check.
Fixes are as follows:
1. in ncdump.c and nccopy.c change all occurrences of
   'return EXIT_FAILURE'
   and
   'return EXIT_SUCCESS'
   with
   exit(EXIT_FAILURE)
   and
   exit(EXIT_SUCCESS)
   respectively.
   I have no idea why this works.
2. in libdap2/ncdap3a.c#freeNCDAPCOMMON,
   remove the call to nc_abort, it is
   causing a loop; not sure why this
   is not caught under other operating systems.
Merge branch 'master' of http://github.com/Unidata/netcdf-c
Updated developer doxyfile to automatically parse the '.doc' and '.md' files present in man4.
Updated RELEASE_NOTES.md with reference to Jira ticket for DAP/Cygwin64-related bugfix.
Updated documentation in preparation for upcoming 4.3.1.1 bugfix release.
Corrected a markdown/doxygen syntax issue.
Fixed some markdown syntax errors on the 'building with cmake' document.
[NCF-287/MCI-552767
Problem related to NCF-284.
Namely an old thredds server that
does not properly implement the
dap2 spec. It is accessing a field of a grid
but is not wrapping it as a structure.
url:http://thredds.aodn.org.au/thredds/dodsC/IMOS/ACORN/gridded_1h-avg-current-map_QC/SAG/2010/01/27/IMOS_ACORN_V_20100127T023000Z_SAG_FV01_1-hour-avg.nc.dds?SPEED.SPEED

In any case, this exposed another bug.
Also, in looking at this, I realized that the
code could be simplified.
Merge branch 'master' of http://github.com/Unidata/netcdf-c
Updated .gitignore to remove filter on autoconf files.  This messes up our release process on github.
Added CTest specific files (previously missing) to Makefile.am so that they would be included by 'make dist'.
Added CMakeLists.txt to missing Makefile.am files, so that CMake-based builds can be used on source packages generated by make dist
Added missing test script to EXTRA_DIST in makefile.am.
Resolved Conflict when cherry-picking patches.
Replaced missing character.
Updated CMake file.
Updated release notes to mention a JIRA issue that Dennis has addressed.
Created a base pkgconfig template for cmake from the autotools file.
Stopped tracking a cmake-specific pkgconfig template; using the same one as autotools. Tightened up cmake summary a little, now a pkg-config file is generated.
Corrected some warnings issued by doxygen when generating documentation.