switch to run_shell_cmd where possible in easybuild.* modules
#4430
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Only remaining usage of
run_cmdineasybuild.*are those whereasynchronous=Trueis used (which is not supported yet inrun_shell_cmd)Changes to
test_index_functionsare necessary because arun-shell-cmd-output/*/out.txtfile located inself.test_prefixwas making the test fail (which doesn't make sense)