Several fixes

- fix bug with empty source not being detected in 'options'
- fix issue with explicit dependencies not working when there were no
dependencies in the code
- fix issue where code has empty define() call
- check whether dependency exists and is a file (i.e. not a directory)
- wrapper for StubStrategy now wraps items in a function and calls that
function (previously did not call the function)
- interpret one command line option that ends with yaml, yml, or json
as a configuration file
- check for 'ignore_missing' option in tests
- deploy w/increment to version number