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If you have other ppl than yourself that uses the software a good option is to limit functionality as much as possible until they request it. One good way of limiting the problem with users uploading files into the configured root folder (usually a website root) is to limit write access completly to that folder, but not sub folders.
Place a file named mc_access into the configured root folder and fill it with this content:
_filesystem.writable=false
_general.disabled_tools=createdir,createdoc,refresh,zip,upload,edit,rename,cut,copy,paste,delete,selectall,unselectall,view,download,insert,addfavorite,removefavorite
The underscore “_” forces the option to be local and not continue to apply to all sub folders.
Each configuration option in the wiki will contain example on how to use the config option inside an mc_access file.
This is quite a nifty feature, when a user creates a folder, you can use directory templates in order to control what that folder can do and contain, that means you can put an mc_access file into a directory template! You might want to have a complete folder with sub folders when your user creates a new folder, so he knows where to put images and documents. Perhaps you want a certain index file, or empty submenu file to be included with every folder if you use it to control structure, submenus and layout.
You can checkout the configuration option in the wiki, also don’t forget that you can force your user to use these directory templates, and of course, if you configure using mc_access you can have different directory templates depending on where the user decides to create a new folder.
There is also an option for using file templates in MCFileManager, will copy a template of a file when a new file is created.