Sorry for the delay.
Unfortunately we're not going to be able to support scripts that haven't been created using SQL Source control, or SQL Compare.
We may be able to read the scripts in, but we would end up writing them out to new files based on our own naming convention. This would end up loosing the history.
SQL Source control (and SQL Compare) only support scripts that are organised in a certain way. For example, if SSMS writes out objects like triggers to separate files, then we wouldn't be able to handle it.
We could add support for scripts created by SSMS, but as there are so many different configurations you can use, it would be a nightmare to support all of them. So far there doesn't seem to be much call for supporting SSMS scripts.
Sorry I can't really give you a workaround for this.