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

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

Use the primoridal Helium abundance to compute the Hydrogen mass fraction. Optionally read the temperature transition from the YAML parameter file.

Make reports a little less specific

Add a new parameter to the gravity calculation to control the frequency of the tree rebuild using a fraction of the number of gpart updates.

Improve the way we define the time of the first snapshot and statistics in cosmology and non-cosmology modes.