When merging files from different branches, fossil says it's adding a file but is only checking it out without adding it to the manifest. Test case:

<verbatim>% fs branch list
  branch1
  branch2
* trunk
# The following version was for a checkin on branch1
% fs up 9c21f3ec0f foo.txt
Autosync:
                Bytes      Cards  Artifacts     Deltas
Sent:             130          1          0          0
Received:         446          9          0          0
Total network traffic: 340 bytes sent, 0 bytes received
ADD foo.txt
--------------
updated-to:   2011-03-06 10:16:14 UTC
tags:         branch1
comment:      Create foo.txt on branch1 (user: user)
"fossil undo" is available to undo changes to the working checkout.
# Based on the above output, I would expect foo.txt to have been added to the repo
% ll
total 1
-rw-r--r--  1 user  user    0 Mar 10 09:50 foo.txt
% fs stat
repository:
local-root:
server-code:
checkout:     2011-03-08 10:03:46 UTC
parent:       2011-03-08 09:56:13 UTC
tags:         trunk
comment:      Some checkin msg. (user: user)
% fs add spammers.pftable
ADDED  foo.txt</verbatim>