RoboHelp HTML 9 Webhelp Layouts include all (unnecessary) project files

I am currently using RoboHelp HTML 9 on Windows 7 Pro. I have administrative rights on the computer.
My current project contains over 30 different webhelp layouts with 30 different TOCs that are all based on the different functions in a web-based application for a client. The project also includes over 30 different print layouts based on the same TOCs. I use build conditions to specify what I want to appear in the webhelp and print layouts. My project is organized into basically three main folders that represent Tasks, References and Concepts (as close to DITA as I can get this client). Each of these main folders has a subfolder named after a function and it contains the topics and screen captures that relate to that specific function task, function reference or function concept.
I created each webhelp layout in the SSL pod based on the specific TOC that was created for the function. In the WebHelp settings, I specified the TOC in the Content section along with enabling the "exclude unreferenced topics from output" and "exclude unreferenced baggage files from the output" options. In the Navigation section, I selected the appropriate skin that I customized along with enabling Contents and Search options with adding the About box.
With these settings my problem is that ever single webhelp layout includes all of the files in the three main folders, even when they are not referenced in the TOC. This has caused my outputs to explode in size because of the unnecessary folders filled with files (topics and graphics). How can I compile the webhelp layouts so they only output the files referenced in the TOCs and not every single file in the the three main project folders?
Any suggestions will be greatly appreciated because my client is not local and I have to send these files to them over the internet.
Thanks in Advance!

"Exclude unreferenced topics from output" starts by excluding topics that are not in the TOC etc. However if a topic in the TOC has a link to a topic that is not in the TOC, the linked topic will also be included to avoid a broken link. It also daisy chains so that if the second topic has further links, that too gets included.
The idea behind this option was that people wanted TOC only outputs but Adobe chose to implement it in this way. I can see why but I take the view that if that results in broken links, that is the author's responsibility. If you agree, then please follow this link and ask for true TOC based authoring.
http://www.Adobe.com/cfusion/mmform/index.cfm?name=wishform&product=38
Meantime you will, as Amebr points out, need to create build tags and expressions. There is a page on my site that covers that.
See www.grainge.org for RoboHelp and Authoring tips
@petergrainge

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