Fix possible unnecessary rebuild

This fix the unnecessary rebuild in the following scenario:
A package rename its manifest package name and the old R.java was still
in its intermediate dir. The rule to generate R_file_stamp may always
copy the old R.java with timestamp reserved and the R_file_stamp never
gets updated.

Change-Id: I659cbb00f0e7734d7d71e1ca66065f587c8dee2c