removing some magic from the cli, making all arguments treated the same

this aims to simplify the CLI as described in #400:

 * no longer automatically piping to stdout for a single entry (for consistency)
    * when using `stdin`, using `stdout` is implied and still works as before
    * the `--stdout` flag has been added to specify stdout
 * removing the implicit 'output' dir as the last argument
    * the already available `--output` flag should now always be used
 * expanding folders via `glob` into a list of files (arguably magic, but predictable)
Merge pull request #406 from duojs/simplify-cli

Removing some magic from the CLI