It appears that only locally loaded files are visible for iCloud folders in 10.15 Catalina. This had not been a problem in 10.14 and appears to be breaking numerous applications.
Notice which files here (Sorted largest first) are not local (Little cloud symbol)
and which files are visble to /bin/ls
Notice that the first local file in the Finder is dratisDifference.js and that the second is an iStock photo containing 82.100. These are the first two files discoverable by ls. It's not that they are in a different location in the sort order. They are not visible to ls at all. They appear not to exist.
This appears to be the cause of many problems for applications (github, IDEs etc.) running under 10.15 where files are just found to be missing from the file system.
