Stop ignoring classes on the classpath for stubs

We're working on moving the libcore classes away from srcs and into the
classpath, and ignoring classes on the classpath will cause incorrect
API signatures once that happens (several libcore classes appear in
public API signatures).

Keep the docs building in the same way they were before. They will be
addressed in separate CLs.

Bug: 173606718
Test: m checkapi
Change-Id: I471327c3657662d7a093e9baa2fb6e08d640f895