Harden file reading

[bennybp]

Reading of input files and test files has been greatly improved by commit 98887f300ca836c0d8c3ac597914936096aae678, but is still fragile. That is, malformed files will often generate an incomprehensible error much later in the file, which is hard to debug (by and end user).

This is somewhat low priority, but is still important in the long term

• [ ] Rewrite file reading routines to check for proper number of columns in a line
• [ ] Apply this to reference files as well