Jalview args CLI skips last format and outputs multiple files with input format

logic in Jalview.java for final arguments processing reads two args at a time -- fileType and fileName. Fine for image types, but when it comes to actual alignmnt output, it skips the fileType just read and uses the input format instead.

Variable "format" is being used instead of "outputFormat", and no check is done to see if the format is valid.

Because there is no test, and because there is no break statement, any unidentified/misspelled arguments are collected and used for filenames for unwanted file saves.

Jalview-JS/develop has a retooled section of this process that uses switch instead of multiple if/else blocks. For reference at least.

CR to be attached momentarily.