I can't find any action on the project in the Java Api, such as create, modify. Does the Jira software Java API provide operations on the project ?
It depends which operation you're looking for, but this page should be a good start.
I do not think we can answer that usefully. "Create" and "Modify" very much are supported by the REST APIs and have been (albeit SOAP for older systems) for almost 2 decades.
There is a lot of stuff supported over REST, but a lot of things that are not too. Could you explain what you are trying to do (over REST) in some more detail please?
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