Convert test that disallows non existent paths to use fixtures

This change needed to add some additional files to the registered
files for PrepareForTestWithJavaDefaultModules because otherwise they
would fail when "TestAllowNonExistentPaths = false". Those files were
being added by the TestJavaLintRequiresCustomLintFileToExist (albeit in
some cases in different locations to that required by the default
modules but as the files are needed by the modules defined in
PrepareForTestWithJavaDefaultModules they should be defined in it.

A couple of other places also provided some files so moving them into
PrepareForTestWithJavaDefaultModules caused some conflicts which needed
to be resolved.

Bug: 183184375
Test: m nothing
Change-Id: I76ce9f1673c1c1c4000635b76b8377d582224bf1