deprecate run_cmd and run_cmd_qa & co, move them to easybuild._deprecated module

[boegel]

All code in easybuild/_deprecated.py was cut from easybuild/tools/run.py without changes, with one small exception: the run_cmd_cache decorator was changed to only consider inp, not stdin (since the latter is specific to run_shell_cmd).

WIP because more work is needed here once the implementation of run_shell_cmd is complete (incl. support for asynchronous and qa_patterns + qa_wait_patterns):

• also deprecate other functions in easybuild._deprecated, like run_cmd_qa, etc.;
• use self.allow_deprecated_behaviour() in tests where needed, or catch deprecation warning to ignore it;