read .in file using the routines used to read .setup files

[danieljprice]

For #513 it would be helpful to read the phantom infile using the database/read_inopts routines that are used to read the .setup file

This should have been done anyway but was always a bit too "big and complicated" to do because there are so many modules using the old style read_options routines with select case and read statements... but it's time to clean this up

Originally posted by @danieljprice in #513 (comment)