AAPT2: Fix regression in Manifest.java permissions

Permissions defined with the same leaf name emit the same
string symbol, which causes collisions. AAPT would override
the symbol with the last one seen.

Do the same thing as AAPT, but emit a warning.

Bug: 64472942
Test: make aapt2_tests
Change-Id: I17b9dc7e8d8bd80db98869394c93695cb453bebd