fix indentation of the rubygem reinstall message
properly register imports for already-processed package sets

There are two codepaths that skip already processed package sets:
 - one looks by repository ID, to avoid re-updating already updated
   package sets
 - one looks by name, to detect name clashes

In both cases, we must update the #imports and #imported_from
attributes accordingly. However, it was only done in the second case.
This commit adds it for the first case as well
renamed README.txt to README.md for github's benefit, update Manifest.txt
validate the formatting of source.yml's 'imports'
start getting rid of Autoproj.osdeps

It is now an attribute of the Manifest object
fix expand_package_selection to also resolve osdeps
remove dead code
updated autoproj_bootstrap to v1.11.0.rc13