I use fossil version 1.29

I have a project where there's a file, simple text.
That file is manipulated by a tool. The tool always keeps the previous
version of the file, renaming it.

So, we have a file 'foo' and 'foo.bak' and whenever foo changes, the
old version of foo is renamed to foo.bak (and the old foo.bak gets
deleted).

The actual repository is on a remote machine and auto-pull and
auto-push are both on, so update and commit both access the remote.

I started with a perfectly synchronised state, everything everywhere was
the latest, the checkout, the local fossil repo and the remote all
matching.

I then ran the tool, so I got a new foo and foo.bak. Then came the
interesting bit:

When I ran 

fossil status

fossil told me that 'foo' was edited, but it kept silent about foo.bak.

Then I told it

fossil commit -m "Some message"

then it complained that foo.bak on disk was different from foo.bak in
the repository and told me two hash-es and then refused to commit. In
addition, in the check-out directory it created a file called
'file-<HASH>' where <HASH> is a hash value in hex.

If I then do a

fossil rm foo.bak
fossil add foo.bak

and try co commit, the same thing happens, except that a new file with
'file-<HASH>' is created, with a different hash value.

I could not commit foo until I settled for 

fossil rm foo.bak

and gave up on keeping track of the backup file.

Is there a rational explanation for the above or should I start
worrying about the integrity of the repo - that would me a major
disaster for the project :-(

Thanks,

Zoltan
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