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Typically I will create a .JS text file that contains my functions and add that to baggage.
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Rick's solution of placing the js files as baggage files seems more prudent. The only problem I have is that these same HTML pages are originally produced from a development program called Sandcastle, and then I import them into my project. There are hundreds of them and they do not have "human-readable" names. The only way I get them to appear in my output is to edit the .hcc file in my project to include the Sandcastle TOC. I would not be able to TOC them manually if they were baggage files...much less reproduce the intricate Sandcastle TOC structure.
Any suggestions as to how I could be working smarter?
You can look into scripting in RoboHelp. You can use a script to import the HTML files and recreate the TOC in RoboHelp. That might save you from manually editing RoboHelp files. See http://help.adobe.com/en_US/RoboHelp/8.0/RoboHTML/WS98613C7C-EF5B-48e9-A91A-D2AABB882687.h tml for more information.