Someone raised an issue against uibuilder that had this error recently. It went away when uibuilder was updated to the current version.
The problem with graceful-fs is that it is embedded in lots of places, especially in fs-extra which is itself used in various places including the Node-RED core and uibuilder.
To track down this problem, it will take someone putting a manual change into their installed version of graceful-fs to trigger a stack dump so that we can see the call chain and work back up the chain until we find the culprit.
Could you also, from the command line, do:
cd ~/.node-red
npm ls graceful-fs
to find out what version(s) are in use?