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I would like to have a section of my document for "Prep" - basically scripting stuff you need to have system wide in order run the document. It's not really relevant to anyone reading the document and I'd like to just have the entire subtree not included in exports. How would I do that?

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As mentioned in my comment, there are tags that can be used to control the export of a (sub)tree: a tree that is tagged "noexport" will (by default) not be exported: e.g.

* Document
** Exported section
This section is not tagged, so it will be exported by default.

** Hidden section                                                      :noexport:
This section is tagged "noexport", so it will /not/ be exported.

The set of such tags is actually configurable, either globally through the value of org-export-exclude-tags, which is just a list of strings, or through the EXCLUDE_TAGS file-wide setting:

#+EXCLUDE_TAGS: noexport hidden classified

You can then use any of these tags to keep the tree from being exported.

As always, the manual is indispensable. These tags are discussed in the Export Settings section.

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