windows line endings in input file cause problems

when the input file has windows line endings, the extra character in CRLF compared to unix gets left at the end of lines when parsed. this causes:

• the expressions for the functions have an extra whitespace character at the end (benign?)
• if using a monte carlo file / user supplied parameter point file, step2 fails to find it because the name of the file has an extra invisible character at the end of it.