[Core] Avoid base64 to prevent malware detection software misclassifying the commands

[Michaelvll]

Previously, we used base64 for the commands to be run on remote machine, which caused malware detection software to misclassify the commands as malicious. We now change it to plain text instead to get around it

Tested (run the relevant ones):

• Code formatting: bash format.sh
• Any manual or new tests for this PR (please specify below)
• All smoke tests: pytest tests/test_smoke.py
• Relevant individual smoke tests: pytest tests/test_smoke.py::test_fill_in_the_name
• Backward compatibility tests: conda deactivate; bash -i tests/backward_compatibility_tests.sh

[romilbhardwaj]

Thanks @Michaelvll! Tested with a yaml containing heredoc and various escape strings in setup, works nicely.