I assume you are referring to this post and thats why you are mentioning agent-base!
well, in that ^ case, it was a node package installed in the palette.
The dir you are scanning is not the userDir
This ^ is the main node-red app install - there will be node modules installed into your runtime in the package for the running node-red project. Often that is /data (or on non-docker, ~/.node-red)
Have a look at your start up log and look out for userDir (probably set to /data)
CD into that and do the same check
In fact, do npm ls and show us what you have in there.
I deleted the two nodes from my project (hope to find an alternative node for dynamic MQTT input later). I restarted the container and the HTTP request works now.