Point PyYAML dependency to official repository

Previously, PyYAML was hosted on BitBucket, so we had a mirror of the
repo on GitHub. Now, official hosting has moved to GitHub, so we can
point to the official repository instead. Thanks to Marco A. Feliu
<marco.feliu@nianet.org> for pointing this out.

This patch also updates the install shim to update submodule URLs. To
preserve the functionality of earlier Dotbot versions, we will need to
maintain 'https://github.com/anishathalye/pyyaml'. Because old versions
of the install shim used with new Dotbot versions will not update
submodule URLs, we will need to keep the old repository in sync with the
upstream repository as we upgrade PyYAML versions.

This patch also upgrades the dependency to PyYAML 3.12.

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