Support access control via adding 'controlled' to folder name instead of file name

[junjun-zhang]

This is a feature request in preparation of hosting large amount of controlled access data files from PCAWG study.

Without this feature, all controlled access files have to be renamed to add controlled in the file name, which is not desirable as files are likely referenced by the original name already.

In the following example, files: file_2.controlled.txt, file_3, file_4 and file_5 are controlled access.

PCAWG
 |__ data_folder_1
 |    |__ file_1
 |    |__ file_2.controlled.txt
 |__ data_folder_2.controlled
      |__ file_3
      |__ file_4
      |__ data_folder_3
           |__ file_5

Also, currently, controlled access file is only visible (listed) when user logs in. It would be greatly helpful, if all files are alway visible regardless controlled or not. Only download controlled file requires logging in.