Staging files deletes them instead if main working tree is not in default location.

This bug has existed in every 3.x version of Sourcetree for Windows (currently still present in 3.4.4) and is easily replicated.

1. Create a repository
2. Edit the config and add `worktree = C:\\Some
   Path` where that path is not the repository directory.
3. Create a file in this new main working tree directory
4. SourceTree sees the new file, but cannot stage it (produces an error)
5. Stage the file with the terminal and commit with either the terminal or SourceTree
6. Change the file
7. SoucreTree sees the change as an edit
8. Stage the file with SourceTree
9. It is staged as a file deletion and the actual file in the working tree is DELETED, along with any changes you were attempting to stage

Deleting files people are trying to enter into version control is a cardinal sin level of bug and this will be my 3rd time submitting over the past 3 years.