Currently this is not possible via the Thesis Abstract plugin, which assumes that the thesis has already been published elsewhere (i.e. a link can be provided to the published thesis). If you like, you can try to extend the plugin by adding the necessary additions to the submit form as well as table structure for the plugin, which is independent of the main OJS code base. You'll find all of the code in plugins/generic/thesis
A good starting point would be to review the regular article submit process, which also includes file upload (submission manuscript) as well as supplementary file upload. You should be able to reuse (with some modifications) much of the code and logic. I've also filed this as a potential future enhancement for the thesis plugin in our bug tracking system
. Please feel free to add yourself to the bug report for comments and/or to submit code if you do have a chance to implement this feature.