Honeycombconfiguration.xml is located in your Honeycomb templates folder, under \\Templates > Honeycomb. When you publish to Honeycomb, Author copies Honeycombconfiguration.xml from the template folder to the publishing folder.
Honeycombconfiguration.xml contains a lot of settings controlling how Honeycomb publishes, most of which you shouldn't change, but you can modify it to add a style to Honeycomb., add a style to Honeycomb.
Honeycombconfiguration.xml's sections
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Honeycomb Settings: Module name, and output file names. Don't change.
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Folders: Don't change
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appsettings: contains a reference to the folder name of the template: hv_src. The name for the template folder can be changed here if needed. However do not change other app settings.
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filpath: you can change the date format, but this makes the file unique. Don't change the remainder of the filpath settings.
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JsonFiles/HTMLTags: Don't change.
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Course structure: Used for generating course.xml.
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TopicClasses:
By default Honeycomb removes all paragraph style names (classes) from the paragraphs. If you want to prevent Honeycomb from doing this, add the style name to this list.
For example, if you have your own special styles, you add them to this list. In the xtend-custom.css you can define the look and feel of these styles.
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Glossary: If your Honeycomb course contains non-Western characters like Cyrillic, you must add these characters to the value for alphabet.
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See Course Completion Criteria for updating the completion values.