Add warning that command is a security concern, make sure output is not mixed with any from the MPI process

-Werror=format-truncation requires this

Add ability to stop the code after a specified amount of time. Also add option to run a re-submission command.

Prevent users from generating gas from the ICs if they are running without the hydrodynamics policy.

Put the checks for i/o dumps into a separate function. Call that function after the 0th step as well.