Yes, "bear arms" absolutely does refer to using them in war. However, since you acknowledge that, it would be somewhat hypocritical of you to consider militias in the U.S. to be domestic terrorist organizations - I'm not saying you do, but that IF you do then it seems to me that you're holding two conflicting opinions.

And do you really think that the Founding Fathers wanted to limit gun usage to military members?

* The 2A was created to protect the citizenry from a tyrannical government, whether it was foreign or domestic; allowing only the government to have guns would work against that.

* You can read the Bill of Rights for yourself and see that all 10 Amendments are to protect the citizens from the government abusing its power against them. Why would the 2A be the only Amendment to grant the government a right?

* Since when does the government/military need a right to own arms? Of course the government can own arms, that's part of it's job. The 2A was created to preserve that right for the people so the government could never take it away.

Also, you're ignoring the part about citizens being allowed to keep their arms.