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Addresses:
#40 Missing and overwritten scaffolding files when scaffolding is already in VCS
#42 .gitignore is merged even if it does not need to be
#43 Add bash scaffolding for project specific bash code during the init command
#44 Do not open preview until the entire init sequence has completed
#47 php install errors when a workspace image is built
#48 Fix and cleanup phpmyadmin
#49 Conditionally create mysql database: laravel
#50 No install of node packages when project is initialized