Choosing shard key and friendly URL Ids for my MongoDB
Before you go further you need to answer a few questions


how do you represent files within folders into the database
how do you represent folders
do you have relations between folders (parent -> child)
how often do you expect to create folders and files
how often do you update existing files into folders and what is the number of files you update


Based on your answers you can have a write optimized schema or a read optimized schema. Write optimized is a schema that contains many entries that are very small
or you can use built in operators like $inc over a collection. Read optimized is generally a larger collection like the one you described, into your scenario you could have very easy something like this (assuming all folders are at the same level)

{ "userid" : "email or id",
  [ 
     { "folder1" : [ "file1", "file2"] },  
     { "folder2" : [ "file3", "file4"] },
  ]
}


But with this schema it gets quite complicated if you need to link a folder to a parent folder ... But is obvious that the userid is the shard key.