It is very rarely a good idea to mess with npm's files. I would have expected the package to appear in Manage Palette and allow you to update it there.
To recover the situation go into your .node-red folder (assuming it is a conventional install) and run npm remove the_package npm install the_package
If there are any errors there then come back here. Otherwise restart node-red and it should be ok.
Eventually yes. I deleted the whole node_modules directory, restarted Node-RED and then installed an arbitrary new palette package, this finally brought Node-RED to reinstall all the packages.
By the time I read it, I had already recreated the node_modules directory.
Running npm install manually in the Node-RED project directory writes files, which might mess up permissions, so that's something I want to leave entirely to the Node-RED process inside the container. Deleting files on the other hand is fine.
Well, of course I am, but even with a host installation from a .deb I would have to watch the permissions, so container or not doesn't really make a difference here.
I believe that the majority of users running node red do not use containers. They generally don't install node-red from a .deb either.
Provided that you are logged in as the user that runs node red then there won't be an issue with file permissions running npm manually. Unless you have a very unusual setup.