This was an issue I spotted in the first Caravel which still seems to be the case. The database unit should be 5 nm. Magic uses this but all the Caravel/Caravan GDS files are configured to a database unit of 1 nm. That makes it really easy to put things off grid which will be DRC violations by the time it gets to Calibre

The units used in a GDS file should not have anything to do with the minimum manufacturing grid. Do you mean to say that there is a tool that believes that if it read a GDS file with units of 1nm, then it also believes that the minimum manufacturing grid is 1nm?

Yeah, in klayout if the grid is set to 1 nm then you can move objects in 1 nm increments. As a result if you move anything you invariably end up off grid. I set up my main klayout file with 5 nm grid but today I started putting designs into the user_project_wrapper which is 1 nm grid. So I had to change grid size and scale some things. I'm also not confident that the combination back into caravel will be smooth now because the wrapper has changed grid size from what is expected