Adjusted subprocess.run() calls to use arg list, rather than string.

The Python docs recommend passing a sequence to subprocess.run() when
possible. Doing so allows for automatic escaping and quoting of
arguments.

https://docs.python.org/3/library/subprocess.html#frequently-used-arguments

> args is required for all calls and should be a string, or a sequence
> of program arguments. Providing a sequence of arguments is generally
> preferred, as it allows the module to take care of any required
> escaping and quoting of arguments (e.g. to permit spaces in file
> names).

Also removed `shell=True` where unnecessary. 

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