[ENH] add ability to apply patches to Tiki codebase and 3rd party vendor packages

This enhancement enables managing patches applied to an instance. Patches are applied via the gnu patch utility. For now, deleting a patch doesn't revert the patch - manual work is needed to actually revert a patch. Added instance:revert command to revert a particular instance working dir to its original branch state (aka git hard reset) - only works for version controlled instances.

Also, code was added to make sure patches are applied on certain events in Tiki manager - e.g. after restoring an instance from a backup, copying the source instance patch list to a cloned instance, etc.

@rjsmelo @xorti I tried running the automated tests locally but src/env_includes.php was missing. Added that one setting env variables like TESTS_BASE_FOLDER, SSH_HOST_NAME, etc. but still a lot of the tests fail with errors - I think I don't have the proper test env set up. Can you please send instructions on how to run the automated tests or maybe update the README and/or add missing env config files? Thanks!