Plugin Registration Tool accepts only one assembly (dll) to upload. If you have third-party dependency assemblies like Newtonsoft, you have to combine with some assembly merging tools such as ILMerge.exe.
You might probably know, there is a Team Member license for Dynamics 365 CE which costs $8 as opposed to full user cost of $115.
You might wonder how a team member license is different from a full user license.
As per Microsoft Licensing Guide, Team Member