:bug: Make MessageRegistry::deleteMessages work for both type of linters
:bug: Make MessageRegistry::deleteMessages work for both type of linters

shawninder/linter,DanPurdy/linter,e-jigsaw/Linter,blakeembrey/linter,levity/linter,AsaAyers/linter,Arcanemagus/linter,atom-community/linter,JohnMurga/linter,steelbrain/linter,AtomLinter/Linter