I propose creating a separate eclipse project for the trunk and each branch.
It was easier for me to merge and tag when the branches are split. In addition, updating one project will take longer than allocated projects, as you will have to check for new tags that you create each time.
One more note: Eclipse is based on Java. Checking the entire code base as a single project will significantly affect the performance of your system. When projects are split, you can simply close branches that you are not working on.
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