Just to make it clear to readers of this question, I found out what the problem was. The new version of Atom was not installed properly in that sense that the old version of Atom was still in place although I erased it. I did reinstall the new version of Atom and did the following using the the command line in terminal:
apm uninstall ink
apm uninstall julia-client
apm uninstall language-julia
apm uninstall tool-bar
apm uninstall latex-completions
apm uninstall indent-detective
apm uninstall uber-juno
to make sure there are no old Julia-based Atom packages lurking around. Then install Julia-based Atom packages with the following commands:
apm install uber-juno
apm install ink
apm install julia-client
apm install language-julia
apm install tool-bar
apm install latex-completions
apm install indent-detective