This took me a few hours to figure out and gave me a good scare. I finished spending ~6hrs working on the same file doing a large refactor and this error had me in a panic for a while. Here's the reproducable test case.

<pre>% alias fs fossil
% echo old >> foo.txt
% fs add foo.txt
ADDED  foo.txt
% fs ci -m "Add foo with 'old' content" foo.txt
New_Version:
% fs mv foo.txt foo-old.txt
RENAME foo.txt foo-old.txt
% echo new > foo.txt
% fs ci foo.txt
fossil: fossil knows nothing about: foo.txt
Exit 1
% fs add foo.txt
ADDED  foo.txt
% fs ci -m "This won't work" foo.txt
New_Version:
fossil: manifest file (5) is malformed
Exit 1</pre>