Gromit does not document the required files for each step

[jbarnoud]

When running gromit from a latter step than TOPOLOGY, it is impossible to know for sure what files must be present by reading the documentation. The only way to know is to read the source or to navigate through error messages. This is especially an issue as some requirements are not trivial. For instance, when starting at the EMVACUUM step, the user needs to provide $base.gro via the -f argument so it can be used to define $base and to produce the Solute group in the index. The user must also have $base-pbc.gro in the directory as it is the output of the previous PBC step and the input of the EMVACUUM step.

A list of expected input files would be beneficial in the documentation.