Fix strict setting to be consistent throughout the pipeline.

I originally changed the configuration of strict mode to be on
a per project basis in the user configuration, because the user should
be able to set their preference on a per project basis.

I however made the mistake to make the strict mode be considered
on a per project basis within a single pipeline, this commit corrects
the behavior such that when you are building a project with junctions,
only the toplevel project is considered when deciding strict mode
for the whole pipeline.