Possible fixes:

1. Fail early with a clear error message.

2. Automatically revert files that are MISSING

3. Automatically "rm" or "del" files from the check-out when they go MISSING

anonymous added on 2009-12-16 17:28:38:
In my opinion, "commit" should fail early and clearly. "Update" should do an automatic revert (with a printed line notifying the fact), for all files that have not been "rm'ed" from fossil. This is nothing more than saying that the merge algorithms do the following:

a) 2 ascii files: automatic merge

b) 2 binary files: error

c) 1 file in fossil and nothing in user checkout: automatic revert

anonymous claiming to be Michael McDaniel added on 2009-12-16 20:20:11:
I disagree with automatic revert unless it requires an explicit flag.

I may have just reorganized my project, removing many files and subdirectories. Perhaps I forgot to do the 'fossil rm'. I would not want to watch all of the files and directories re-appear automatically. I would prefer that a --force flag (or some flag) be required before (possibly many) files (and possibly subdirectories) are repopulated into a working directory.

drh added on 2009-12-18 00:31:46:
Fixed by 76f169fca6c040496b14bd37a9e2c5e00f0a797b.