install server applications from repositories
The whole root thing drives me crazy - but i hear your reasoning. Need root to install various packages. why not let users install packages from set list of repositories ? you can always block certain ones.

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imisterk commented
That would be great. Ability to add our own custom Application packages together or from pre-made repositories would be great.
I often find an important use for certain Wordpress plugins which I install on every deployment. For example custom css plugins, better search replace, security audit log and so forth.
Alternative way is to create a clean application with your custom modifications and then cloning that application on each new project deployment. That said, you will have to keep those custom modifications always up to date which is bit of a pain in the ass.
What about opensource repositories created by the Cloudways community? Then simply add rating system/reviews so that we know they are safe/good to use?