* Reorg and update options for doc and cmake config
* Correct subfiling depends
* Add linux S3 binaries to GH published files
* Correct path
* Try reducing parallel jobs in tests
* Change examples jobs for test from 8 to 4
* Merge examples repo into library
* Change grepTest to be more fault-tolerant
* Update examples macro file
* Exclude all Fortran examples from doxygen
Fixes a few issues created in #3580:
* Fixes a problem where committed tools test files were deleted when cleaning after an in-source build
* Fixes issues with test file paths in Autotools tools test scripts
