anonymous claiming to be seanc added on 2012-11-03 23:08:57 UTC:
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.

% 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: 74332f59163ade09a83448a86ad20cf68e443805
% 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: a75fbcde19942395fe638a4c7dddd18bc995262a
fossil: manifest file (5) is malformed
Exit 1