magic: fix scaffold.includes handling if autodoc disabled

In particular, do not add AutoDocMainFile.xml to it if
we do not create that file.
Update package version
remove last traces of gap/AutoDocEntries.g
Remove 2nd CreateAutomaticDocumentation param name_documentation_file

Actually, it was already being ignore; but now it is also undocumented,
and it can be omitted (but for backwards compatibility, we still
allow you to pass it in).