remove binary / util paths from monkeypatching

[philipmac]

all utility paths can be defined in .env files on machine to test / run
There's no need to have >1 path for test vrs run
which does not really address this issue
The developer should initialize every utility one time, in env files. If these files are not existing a preflight check in the test should warn / fail.

[mbopfNIH]

Agreed. Using .env files for paths is better than util.which, which also didn't work on HPC. In the case of executables not being available, a "fail fast" approach is probably warranted.