Currently, Repackager does not have built in command line functionality to build an .inc file to an .msi file via the command line. It must be done through the IDE. We do however have an internal utility that we use that can do this. I've attached it for your convenience.
Let me stress, we do not support this executable as it has not been tested by us. But it has been used by our QA team for some time now with success & you are free to use it at your own discression.
The file must be placed in the same directory as your isrepackager.exe file, usually
\adminstudio\\repackager.
Help on using it can be found using the /? switch at command line.