For some reason I don't know why JDeveloper is blocking file creation and editing. I'm not even able to create new projects. The image below shows all files with an yellow lock (which I've never seen before). My project in JDeveloper
I do not know why it happens but happen with me and I have one kind of solution.
After you restart JDev you will be able to create files and edit files in your project.
There is a bad side of this solution. You will lose your IntegratedWeblogicServer and all your configurations on JDeveloper.
For that, I have a tip that I used to do as well. From time to time I just copy the entire "system12.1.3.0.41.170120.1047" to a folder that I call "system12.1.3.0.41.170120.1047.backup". When this problem happens I just delete the "system12.1.3.0.41.170120.1047" and copy "system12.1.3.0.41.170120.1047.backup" to "system12.1.3.0.41.170120.1047". Doing this I just lost a few configurations not everything I had.