Rebuilt scanner and options and report naming

[notian]

• Convert the scanner to a Directory Iterator
• Removed the skip blank lines to allow for correct line numbers
• Added trim of whitespace to skip tab/space only lines
• Converted options to use getopt so that "-f file" is valid as well as "-f=file"
• Changed report filename to start with project instead of timestamp for easier sorting/tab-completion

[joeparsons]

This fixes #39.