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
Merge branch 'stable'
run 'gem pristine' only for the gems we know and use

gem pristine --all --extensions is broken for gems that are installed
via a prebuilt binary package that contain a C extension. In this case
rubygem tries to build the extension and of course fails as it does
not have the rights to the target directory.

This commit modifies autoproj to run pristine only on the packages we
know about (i.e. the rubygems we depend on). It modifies the mechanisms
so that other os-indep managers (e.g. pip) can provide the same service.
fix --no-deps when running autoproj update
fix handling of relative paths in autoproj show

CmdLine.initialize_root_directory was chdir'ing into the root dir,
which was breaking the expansion of relative paths. This commit
expands before calling initialize_root_directory
remove long-unused flag
fix configuration update when --from is given
move most of the toplevel functionality into Ops and separate objects
remove deep handling of ignore_dependencies

ignore_dependencies was handled at the level of the autobuild package
code, which has proven to be really really unreliable (on top of
begin ugly) as it misrepresents the configuration.

It is now expected that each subcommand that accepts the option
handles it explicitely
do not chdir() in the root dir anymore

All operations should now be done relative to root_dir anyways
remove accesses to global methods systematically
make autoproj update a subcommand
go on with modularization