Patterns add new attributes, and they add them to the GUI using model.addDisplayAttribute(), or by using the older method which is something like adding them to the tw_meta_data_attrs list. Not sure that is the exact name of the list.
It is preferable to not customize the taxonomy if you can avoid it.
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There is no need for addDisplayAttribute or adding via tw_meta_data_attrs to see the ad-hoc attributes in the query-builder.
Simply adding an ad-hoc attribute to a node will add it to the list of things for the query-builder for that node
If all references to a given ad-hoc attribute are removed, the ad-hoc attribute will remain in the query-builder list until a re-index of the datastore is done.
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This list comes from all nodes of that kind which have ever existed and been given that attribute. The datastore remembers this information.
Not all attributes appear in the taxonomy. That would require lots of changes to the taxonomy with little real benefit and mean that whenever users wrote patterns they would need to also update the taxonomy.
Thanks everyone for the replies! My guess was that is was simply pulling attributes from database but I don't like giving out an answer unless I know for a fact that I'm right. Now I know.