I am trying to check in a file that does not exist in the branch but I keep 
getting told that it "is already under version control".

I tried creating a brand new branch and even tried renaming the file but I 
still get the same message. I tried with a different file and didn't get 
the message so it is something specifically about this file, two things 
which may be of relevance:

1) It was previously checked in but to a different branch and has since 
been deleted from that branch. The file I am trying to check into this new 
branch had been placed onto my computer by syncing, then copying/pasting. 
Is there therefore some metadata somehow attached to the file which 
Versions can see and is thus preventing it from checking in? 

2) It is an Xcode workspace file and thus not really a single file and in 
OS X these types of files are bundles which are therefore actually folders. 
However I have had no previous problems checking in this type of file 
before.

Version 1.1.11 on OS X 10.7.5

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