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Things to watch out for when copying and moving files around Collab...

Permissions and Windows Fileshares

When copying a file (copy/paste) or moving it (cut/paste) from one volume to another (e.g., from Collab to Home), the file will lose the original permissions it had before the copy/move.

So, for example, if you copy a file, mystuff.txt, from Home to a directory on Collab accessible to everyone in your department, then anyone in your department will able to access the file on Collab.

The same is true if you copy/paste a file within Collab, say from a directory accessible to anyone in your department to a project directory accessible to a specific group of people, some of whom are outside your department.  Once copied to the project directory, the file will be accessible to the specific group.

This should all be fairly intuitive.  Files take on the permissions of the containing directory.

There is a gotcha, though.

If you move a file (drag and drop) rather than copy it, then the file retains its original permissions, but only if it is being moved within a single volume (e.g., from one part of Collab to another; not from, say, Collab to Home).

Why does this matter?  Because if you are reorganizing lots of files and you cut/paste or drag/drop files with special/individualized permissions from one place on Collab to another, they will retain their original permissions.  Say you cut a file on John's folder on Collab that has files in it that only John and Bob can see, and you paste them into a general department-wide folder on Collab.  In their new place, the department-wide folder, they will still only be visible to John and Bob.  If you want the files to become visible to the entire department, copy and paste them, then if desired delete them from their original location.

See Microsoft's Knowledge Base document, https://support.microsoft.com/en-us/kb/310316, which states that

By default, an object inherits permissions from its parent object, either at the time of creation or when it is copied or moved to its parent folder. The only exception to this rule occurs when you move an object to a different folder on the same volume. In this case, the original permissions are retained.

Examples:

SourceDestinationOperationResult
HomeCollabCopy/PasteFile Takes on Permissions of Parent Directory
HomeCollabDrag/DropFile Takes on Permissions of Parent Directory
HomeCollabCut/PasteFile Takes on Permissions of Parent Directory
CollabCollabCopy/PasteFile Takes on Permissions of Parent Directory
CollabCollabDrag/DropFile Retains Original Permissions
CollabCollabCut/PasteFile Retains Original Permissions