This commit migrate tests not targeting autotool to cmake.
* removed openthread-test-driver
* removed functional tests from autotool based check
* corrected file permission of python scripts
* added --run-directory to specify directory to collect logs and captures
* get test-ot-test-srp-server pass on POSIX platform
This commits updates `thread-cert/Makefile.am` adding some existing
tests that were not included in the Makefile when the tests were
added. It also sorts the entries to be in alphabetical order.
This commit also updates the access control mode for all script files
to be executable by all (`chmod 755` or "-rwxr-xr-x").
Yakun Xu