Pass stages to StageRunner#configure_and_apply explicitly

[#54320562}
Add .ruby-version file (1.9.3-p448)
StageCollection has OS and Infrastructure stages
Run serverspecs against the stemcell chroot

[#54320562]
Consolidate package instalation into base_apt

Signed-off-by: Tony Hansmann <thansmann@pivotallabs.com>