Clone all modules between mutators and GenerateBuildActions

A common pattern in mutators is to set a property on a module to be used
later in GenerateBuildActions.  A common anti-pattern is to set a member
variable instead of a property.  Setting member variables will appear to
work until a mutator calls CreateVariations after the member variable is
set.  The first variant will have the member variables, but any other
variants will have zero values for all member variables.

To catch this common case early, replace all modules with clones after
running all the mutators but before GenerateBuildActions.

This catches the anti-pattern used in bootstrap, replace the buildStage
member variable with a property.

Change-Id: I6ff37580783a6227ebba2b46d577b443566a79bb