[HostStubGen] Fix off-by-one bug when incrementing index counter

This bug will cause the first element of the zip file to be skipped.
Applying jarjar on the output simply reorder some classes to the first
element, making the bug more apparent.

Also, take the opportunity to fix concurrent logging bugs

Bug: 414920323
Flag: EXEMPT host side change only
Test: atest RavenwoodCoreTest
Change-Id: I43d25eeea10d7a611d0474fd9a270823a48199d7