They should be separated tags. If users are confused about their use is our responsability to guide users into the light.If users are confused about their use is our responsibility to guide users into the light. That most of the users don't recognize the differences between them and we leave them like that just promotes the confusion in all the users that has the right to know how each of the parts of their system is called and will facilitate the exchanging of information between the users to answer and ask questions.
A fine tag excerpt and tag wiki explaining in plain english what are the uses of each tag and how to use them will be beneficial.
No other SE site merged command-line, shell and terminal. Both Super User and Unix & Linux use separated tag and command line is present only in 5% of the terminal and shell tags in SU; and in U&L only 10% of the tags has relationship.