I am trying to install a newer version of ayon-core to the server to use a new feature, however, on running the dependency tool to create the dependency package and deploy it, I am facing the error below:
With latest ayon_core you should disable the openpype addon since it replaces it. Does that already solve it for you?
Make sure to set openpype addon to None in the bundle when you’re working with ayon_core on 0.3+ or something (not sure when it started replacing openpype exactly, but I believe 0.3)
For separate addon repositories, then yes - you do it per addon.
Whilst now there are quite a few still in the ayon-core repository you can create the zip packages for those addons easily from ayon-core repository:
Ayon core:
ayon-core/create_package.py
Ayon core addons that are still in the repo, like ayon_maya, ayon_houdini, etc: