Currently, it's possible to drag and reorder queries. I think it makes sense to be able to do the same with transformers.
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@nacho thanks for bringing this up! It's definitely on our radar and we'll let you know when we ship it 
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It would be nice to create folders as well and store them there! For big projects I can have like 40+ queries and transformers (which can get kind of annoying having to scroll through)
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@mrgnhnt96 Query Folders are up in the queue as well!
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When Query Folders shipped, this request also was resolved since transformers and queries are together in the same list!