Revisit and refactor AlignFile/FileParse input stream close/dispose semantics

Ideally, any low level file ops should happen in the base class (FileParse) rather than in AlignFile. AlignFile should call the FileParse.close() method rather than directly manipulate dataIn, which is managed by FileParse. Note that FileParse.close() nulls the dataIn reference so the stream can be garbage collected properly.

It's also good practice to try to close() in a finally {} clause, catching and reporting exceptions if needed... this is actually what the FileParse.close() method's design was intended for, since the caller should have already checked 'error' and 'errormessage' for parsing problems. Exceptions/Errors on close are not fatal for file import, but could be useful to include in debug/trace logging.