[ACCEPTED]-Adding git submodule into the root of the repository?-git-submodules
Clone the submodule into a subdirectory 3 and symlink it's contents.
For pathogen, I also 2 explicitly blacklisted itself (in the bundle directory) to prevent 1 it from self-sourcing.
You can't have a submodule at the root of 3 your repository because both .git folder 2 would conflicts.
You must create your submodule 1 in a subfolder.
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