Use new flag for emma instrumented build and limit to apps only

Based on existing setup, when EMMA_INSTRUMENT is used on a full
build, all Java modules will be processed with emma instrument
unless otherwise marked in their own Makefiles.

For the purpose of collecting code coverage, emma-instrument
all Java modules aren't that useful, instead, instrumenting all
the app packages is more useful. This change adds a new flag
EMMA_FULL_APP_INSTRUMENT, which can be used with a full build
to instrument all app packages.

Change-Id: Ie143fed49c23402b21f6cccac2ef25741726be45