Store ninja file deps from PackageVarContext in the config

Store ninja file deps from ExistentPathForSource on a
PackageVarContext in the config instead of the PackageContext, as
the PackageContext may be shared between multiple tests running
in parallel.

Test: all soong tests
Change-Id: Ib1809a4dd4a82696e0fe48a87eac21a44684ecb5