Well, I came with one solution of the problem. 
As long as it can be useful for someone else, I will describe it here.

The trick is to use as --baseline the first check-in of the subproject
that have unnecessary files striped. For my case, I simply tagged this 
check-in with "OnlyFreshLib" tag and now the proper merge sequence for 
trunk branch becomes following:

fossil co trunk
fossil merge --baseline OnlyFreshLib FreshLibDev
fossil commit

Note: The problem in details and the structure of the example repository 
is described below, in my previous message.

---------- Original Message ----------
To:  (fossil-users@lists.fossil-scm.org)
From: John Found (johnfo...@evrocom.net)
Subject: [fossil-users] Question about best practices with Fossil.
Date: 3.3.2011 19:22:32

>I am really beginer in the world of version control and project management. 
>Recently I created a repository for one of my projects.
>This repository contains the project "Fresh" that consists of two 
>relatively independent projects "FreshIDE" and "FreshLib". "FreshLib" is 
>actually part of FreshIDE, but can exists as a stand alone product as 
>well.
>So, I created several brances that to make development easy. One of these 
>is "FreshLibDev" where I deleted all files from trunk, but the files of 
>FreshLib itself.
>
>But now I have a small problem. When I change the files in FreshLibDev I 
>want these changes to be applied to the FreshIDE branch (I mean trunk).
>When I try it with "fossil merge FreshLib" from the trunk, fossil tries to 
>delete all files from the trunk, but FreshLib files. "--cherrypick" helps 
>little, because it updates only part of the files. (and I still can't 
>understand which files it updates ;) )
>Now I do the job, using "fossil update FreshLibDev freshlib/*" but this 
>update is not displayed on the timeline graphic tree, and obstructs the 
>comfort following of the changes.
>
>So, at the end the question: What are the best practices to do such things 
>in fossil and what I messed up with the project management?
>
>If my explanations are not clean enough, you can see the repository at:
>http://chiselapp.com/user/johnfound/repository/FreshIDE
>
>Best Regards
>
>http://fresh.flatassembler.net
>Assembly language visual programming.
>
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http://fresh.flatassembler.net
Assembly language visual programming.

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