There is GM9Megascript that deletes a handful of files when cleaning up the SD card. Other than that, no. Many of those files in that kit would need to be manually removed by user preference.
The cfw starter kit is for those who want the convenience of having most of the popular homebrew apps already collected for them, would like to explore stuff they're not familiar with, need a reference setup to figure out which files should go where, and debugging their 3DS systems for miscellaneous software issues.
Of course, the drawback is that the kit is considered excessive to those looking for a simple build where they already know a handful of homebrew titles that they specifically want.
My general reply to noobies with nonworking hacked 3DS systems assumes some of the following:
(1) They followed an unofficial guide such as YouTube video tutorials where their custom firmware setup is incomplete or critical procedures were skipped.***
(2) The setup they're using has outdated arm9loaderhax custom firmware -or- really old versions of [ boot9strap / Luma3DS / GodMode9 ].
(3) Their efforts to revive their 3DS systems has comes up short, and they need a (nearly) sure proof way to get it back to bootable state.
I recommend you hardware test your empty SD card if you've never done so before. The safety of your data and saves will depend on verifying that the card you're using isn't fake or faulty.
You don't have to use the CFW starter kit or all of it. You can pull out only the files specified in the Finalizing Setup, or download them from their GitHub release source page.
Go ahead with Updating B9S if you're not sure or don't know if you're not using the latest boot9strap v1.3.
Do all of the Finalizing Setup. Too many people fail to follow through with the later sections.
First, hack your second or replacement n3DSXL or n2DSXL system using 3ds.hacks.guide. See seedminer or ntrboot for the two most popular methods.
Second, once both your source and target systems have custom firmware, you decide whether you want to System Transfer your first system's NNID over to the second system using System Transfer.
-or-
You can copy or move just the Nintendo 3DS folder with the SDTransfer method. (Ie, you wish to keep the NNID and user profile on the first system but want the 2nd system to have the same set of games as the 1st system).
Thanks for the informative reply. I actually went ahead and completed the tutorial using the CFW Kit. A lot of stuff is on the 2ds that I do not need
I’ve already accidentally opened a program called 3DSbank and now when I boot up, all my games are missing. Then I found them in 3dsBank in one of the folders. How do I remove this? Delete it like I would a game?
I’ve noticed that the 2ds takes a little longer to boot. Could this be because of one of the newer apps from the CFW kit that I installed that I never used to have?
I had another question which I think you answered at the end of your post.
If I just wanted to have a back up of my current console with all it’s games and saves on a separate micro SD card, is it enough just to copy and paste all the contents of the memory card on to another? Or just store on a hard drive?
Thanks again.