The Data directory structure in Sublime Text is very cryptic and confusing. There are highly nested folders such as Data/Local and Data/Packages/User/Installed Packages which serve no purpose of them needing to be nested that way. (Everything could just be in Data since everything has an appropriate extension anyways).
Why can't the whole of "Data" just be the "User" folder as is standard for Portable Apps and get rid of all the nested folders? It is hard for plugins to know if they should look for files in Data\Packages or Data\Packages\User folder. There is no clear way of referencing Data\Packages\User via a variable and knowing if you should reference Data\Packages or Data\Packages\User.
The whole "User" folder is unnecessary since the "Data" folder implies that its a User folder anyways.
Packages should also be able to be loose or zipped in the same folder so that they can easily be worked with and zipped and unzipped during dev time.
A much simpler way would just store everything in Data\ and parse all files in all subdirectories of Data. The default files would be at the following:
/Packages/ - stores zipped packages from vendor
/Data/ - can have zipped packages as .sublime-package files AND can also have loose packages as subdirectories
/Data/Preferences.sublime-settings - User specific settings
/Data/Default (Windows).sublime-keymap - User specific key mappings
/Data/Session.sublime_session - Stores the session
This would greatly simplify the current unnecessarily nested directory structure. If there is any rhyme or reason or necessity to the current directory structure having so many subfolders please enlighten me.