Currently, when I open the Find/Replace window (Apple+F), I see a long list over every query I have saved in the dropdown menu. This is not ideal for me because of the 100 queries, I might only use 1–10 for Project A, 11–20 for Project B, and so on. Is it possible to export and save a group of search queries in one file, a second group in a second file, and so on? I would like to be able to load only the search queries that are relevant to a specific project and have in mind something akin to the "save" and "load" options in the swatches panel and styles panels.
I hope my question is clear, but please let me know if you would like additional information.
Your saved queries are stored as individual xml files in the Find-Change Queries folder in the prefs written in your user profile/library. Queries in subfolders don't seem to show up in the dialog list. It seems reasonable that you might be able to save sets in subfolders, then copy them into the main folder when you want them, but doing it manually would be a major pain. If multi-find/change doesn't do it for you already, it might be worth asking in the scripting forum if anyone could help with a script that would.
I second taking a further look on Automatication's software. If that offers the functionality you are looking for, there is no need to ask in the Scripting forum.
(Even if it does not, it might be worthwhile to ask Martinho da Gloria if it's possible to integrate it. It sounds like a useful addition.)