fix backtrace for warning about Manifest#each_package

I guess it was assumed that the parameter to caller limits the
number of lines in the trace, while it actually removes the first
N-th lines, thus producing unusable traces.
don't warn about the main configuration overriding package set VCS info

This is expected by the user
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
make the gem manager learn how to share the gem cache

If AUTOBUILD_CACHE_DIR, the downloaded gems will go in $CACHE/gems.
This is done through symlinking, unfortunately, as RubyGems has no
API for it.