Brackets looks in several different locations to find extensions to load:
You can view this location using Help > Show Extensions Folder. Normally, this folder's contents are managed by Extension Manger.
disabled folder that sits next to
user has no special meaning for the moment. It's just a convenient location to manually move extensions you wish to disable.
Normally only used when pulling source from Git. This location has advantages over the user folder, for extension developers:
More on How to Write Extensions.
Some parts of Brackets core are implemented as extensions internally, and they are located here. Treat this as you could any other part of the Brackets core code: Brackets may not work properly if you remove or change any of these extensions.
Note: Extensions in this location are not listed in Extension Manager, and Debug > Reload Without Extensions will still load these extensions.