For reference, the patterns for including and excluding files and folders are in âglobâ format.
This means that *
matches any number of characters, including zero, and ?
matches exactly one character. The glob spec states that *
should never match /
or \
, but unfortunately Sublime Text doesnât follow the spec in this regard. In Sublime Text, a *
will match folder_name/subfolder/file.ext
. Normally, one would expect to have to type */*/*
for it to match. It is therefore impossible in ST to reference a base folder without itâs subfolders. 
You can however, match subfolders without matching the base folder, like this:
"file_exclude_patterns": ["scripts/?*/*.js"]
In this example, JavaScript files in the scripts
folder would still appear, but not in any subfolders (or nested subfolders) of scripts
.
To answer your question, then:
As a result of this limitation, you may have to use file_include_patterns
instead like this:
"file_include_patterns": ["*.js?*", "Inner Folder/*"],
the *.js?*
says include all files that end in .js
and have at least one more character following that.
unfortunately, I canât see any way to avoid needing to reference all your inner folders explicitly 
Of course, if you also have non JavaScript files, then this probably wonât help much, as it will only include what matches this pattern. It seems that one canât combine file_include_patterns
and file_exclude_patterns
, nor is it possible to reference the same folder twice, to give different patterns that way.