I meant to put the below text in the initial question:
I've got the 3ds, a9lh, bootstrap, cias, DCIM, fefatesSE, files9, gm9out, hans, hblauncherloader, jksv, luma, plugin, private, retroarch, saltySD, and themes. The folders bolded are ones I'm definitely keeping for modding purposes, but now that I have bootstrap I don't really need the a9lh folder do I?