tl; dr: upgrade setuptools to the latest version and all of these directories will be created in one .eggs directory instead of the root of your project. (Probably greater than 7.0.)
Long story
I came across the same issue after I recently switched from running tox with Python 2.7 to running it with Python 3.4. A Google search found this tox.ini , which contains this dependency specification:
setuptools>=7.0
Since 2.7, I donβt remember having to fight .egg directories. I checked which version of setuptools I had in my 2.7 installation and found 14.3. I checked what I had in my installation 3.4, and found 5.5.1 (yikes!). After upgrading to 14.3 in my 3.4 installation, the only thing I get is the only .eggs directory that contains all the directories that would otherwise be at the root of my project.
I can live with one .eggs directory.
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