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Description
In vim, if there are directories in ~/.vim named "python2", "python3" or "pythonx" vim will look through these directories for python scripts and load them.
:he pythonx-directory
If I have a project in ~/.vim/bundle that has any of the above directories, the python scripts in any of them are not being loaded by pathogen. I tried to look through the pathogen source code but nothing was obvious to me.
While I think they are not used much in regular vim, these directories are critical for making python plugins for neovim. It might be the case that neovim's changes here are incompatible with pathogen or perhaps pathogen hadn't supported these directories before? Here is a discussion with details about how neovim and the pythonx directories work (includes an example of snake in nvim):
https://groups.google.com/d/msg/neovim/VxL0XMu3x18/-zoLfvpOD0gJ
I should mention that pathogen works great with neovim, all of my vim plugins work seamlessly via pathogen. I have not tried to make use of the pythonx directories in regular vim.