As part of my current effort to actually have ships shooting at each other in the near future, I've been working on getting the Friend or Foe lists completed on the Ship Combat Programming page.
Basically, how it works is that each asset you own (ship, colony, or expeditionary force) has a Combat Programming page. At the bottom of this page are three lists: Support, Defend, and Enemy.
If you're in the same location as an asset on your Support List, you'll join in on their side if they attack someone else.
If you're in the same location as an asset on your Defend List, you'll join in on their side if they are attacked.
The Enemy list will not let you automatically attack someone, since I'm going to require you to actually click a button to attack someone. However, it will be useful in giving you more visual indicators that there's a possibly hostile ship in the same location as you, and will probably give you a small advantage if you're attacked by someone on your Enemy list. I haven't worked all of that out yet.
Unarmed ships don't have a Combat Program, other than attempting to flee on round #1 or maybe an option to surrender immediately. I'm still working out the details on that part as well. You don't have to put your own ships on the lists, since an armed ship will automatically Support/Defend other ships belonging to the same player and/or faction.
Here's a screenshot of a current Combat Program page showing the Friend or Foe lists. The top part of the page is still under construction.