Where is the exception to the sixth commandment?

To the best of my knowledge the sixth commandment as given to Moses by God was “Thou shall not kill”, or in a version I found a few days ago the text of this commandment is “Thou shall not murder”. To the best of my knowledge these commandments are shared by Jews, Muslims and Christians. Can someone tell me where is the clause with the exceptions to this commandment that has allowed Jews, Muslims and Christians to fight the cruelest and bloodiest wars in history, all in the name of the same God, which, by the way, goes against the third commandment?