The following forum message was posted by fabioz at 
http://sourceforge.net/projects/pydev/forums/forum/293649/topic/4517189:

The problem is not that the master gets the python nature (whenever you open
a file in a project it'll automatically get it, but that shouldn't be a
problem).

The actual problem is the way that PyDev sees things... inside PyDev, it doesn't
work with the Eclipse abstraction of IFile, and works with actual java.io.File,
so, when it comes the time to show it to the user, it translates that path to
a path in the
Eclipse abstraction to open the editor (sometimes that's possible and sometimes
that's not -- i.e.: things in the system interpreter and not really in an 
eclipse
project, but it should work nonetheless). Anyway, the problem arises when more
than one match is found in the workspace... I guess that PyDev could add a 
better
heuristic to find the proper IFile covering your use case... (i.e.: when a 
duplicate
is found, try to resolve it as an actual python module and if one resolves,
use it, as in your case, although the master has the nature, it shouldn't be
able to resolve it as a module because the pythonpath is not configured).

Please create a bug report for that (you can just point to this thread in the
bug report). See: http://pydev.org/faq.html#how_do_i_report_a_bug

Cheers,

Fabio

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