Add flag to disable source directory includes.

Not all projects can be built when their base directory (the
directory containing the Android.bp file) is automatically included.
For example, external/jsoncpp has a file named version, which will
override the standard library's <version> header.

It would maybe be reasonable for this to be on by default, but many
projects in the tree currently depend on this behavior.

Test: make checkbuild
Bug: None
Change-Id: I58dff2689270ae56fef7cf83be31262d16794fc4