For some reason template system was getting caught up with different

template xml files in some projects. Reverted them, then reset them
back to changes and refresh works properly now. Trevor pointed out
sometimes system gets confused when template file is differet. :/

Please note, the gradle files are ignored and recreated but template
system needs there otherwise it was getting tripped up.

Bug: 63932741
Test: Manually tested samples on physical devices.
Change-Id: If99fecbfebbcafdbfcd740a465535e91af8f6479