Several configuration sections are using separate settings for custom template directories, which can be confusing. This PR adds a new top-level configuration for a custom template directory which is then used for every module. The only exception is the consent templates, since the consent template directory require a specific hierarchy, so it's probably better that it stays separate from everything else.
This PR:
* Converts UPGRADE.rst to markdown and moves the contents into the `docs/` directory.
* Updates the contents of UPGRADE.rst to point to the website instead.
* Updates links around the codebase that point to UPGRADE.rst.
`pandoc` + some manual editing was used to convert from RST to md.
