Commit bfbc47f55e added a lot of those and
this patch tries to cover all that we missed there. Having .md suffixes
in references to internal files makes it convenient to browse the
document locally, just as text files as the references work correctly.
Introduce two main sections "Deployment" and "Usage" and move "Developer
guide" to the top level, too. In particular, split the huge
deployment-and-usage file into multiple parts under the new main
sections. Move customization guide from "Advanced" to "Usage".
This patch also renames "Advanced" to "Reference" as only that is left
there is reference documentation.
