Add more const correctness

Add more const correctness

This helps reduce the size of a future change to how we handle reading
and writing conformation files.

In particular, the way we write symmetric low-level I/O routines that
do both reading or writing according to the value of a parameter
requires that parameters for values to be written are passed as
non-const at some level of the call stack. In several cases, this
change moves that point lower down, so that routines whose job is
writing complex data to files take const parameters. Improving this
helps understand what is going on when e.g. an analysis tool reads in
coordinates, perhaps modifies them, and then writes them. The down
side is that we need to use some const_cast as we get close to the
low-level routines.

Change-Id: I5c22d8681fa5f247f302409bf67b062ebc9fe766