Almost always because two different projects are using shared code from another folder on the system. E.g.
sharedlib/ (symlink to ../sharedlib)
We use mercurial at my company and this is the easiest way to have shared code in separate repositories while still having access to those dependencies from all projects (we have a convention of cloning all of our repositories in a single top-level folder so all relative symlinks work for all of our developers).
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