Cruise missiles are equivalent to what we call "Torpedoes". That is, auto-guided ships with warheads. So you'd like an AI-usable cloaking device. That's a fine suggestion on its own. AI use of cloaks would probably need a mass limit, but that's another thread for another day.
You have clearly avoided the entire point behind me mentioning stealth cruise missiles, the principles behind stealth cruise missiles like the Kh-101 are not exclusive to cruise missiles, the principles that allow stealth cruise missiles to work can be applied to anything that has a radar cross section.
Detection in the current era relies primarily on radar. However, in space, thermal detection and optical detection are also significant. (With optics, not only do you have to hide yourself, but you have to project the image of what's behind you. Detecting background distortions, such as bent starlight, provides significant information on dark elements, such as black holes and dark matter.)
Thermal Imaging will not work in space!
Typical thermal imaging systems can detect temperatures between -4ºF and 2200ºF, space has a temperate of -445ºF, that temperature is low enough to cool down small objects (such as missiles) to below the threshold of thermal detection very quickly, I say again, thermal imaging will not work in space (with the exception of perhaps detecting large astronomical heat signatures that radiate from things such as stars)
And I am assuming that when you say optical detection you mean visual detection, if you consider the size of missiles in StarMade relative to the speed of said missiles (slow in the great scheme of things but fast for its size) then even computer aided visual detection systems will have a LOT of difficulty detection any small object moving at such a speed, the only way I can see visual detection working on missiles would be tracking based on the missiles "tail" but that is not always accurate to the position of the actual warhead.
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As sarge would say: "settle down Francis". Hyperbole aside, this is a very reasonable thing to properly distinguish 'Homing' missiles.
First off, no, this would not negate stealth tactics. Think about it; the alarm is only going to go off after you have achieved a' lock-on' not just because you are tracking your target waiting for the lock. So your first salvo is going to be in transit before your 'surprise' is ruined.
Second of all, if you are cloaked & jammed you can get right up on someone to deliver your missiles or torpedoes as...wait for it...rockets (dumb-fire). Also heat-seekers do not actively ping targets so that is an option too. Each of these variations on missiles (homing, heat-seeking, rockets & torpedoes) have distinctive advantages and disadvantages and are not meant as a one-size-fits-all solution for your combat needs. It just so happens that homing missiles have been getting a free ride so far. There are also countless other weapon options for effective stealth tactics so don't host a funeral for stealth combat just yet.
The only thing that might get nerfed is someones ability to one-shot an alpha-strike weapon at long range, without warning. That is not something worth preserving. Submariners are a crafty lot because stealth is never going to be cake-walk.
[I would approve of the no-alarm policy if target-painting was introduced and used.]
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I'm OK with being able to turn off warnings as a server choice, but still the alarm should be a default for homing missiles lock-on.
To address your statements:
Missiles are slow in comparison to other things in StarMade that have any capability of velocity, that warning gives a pilot enough time to use a jump drive and get a sweet ride a long way away from a missile.
The only way to counter this would be to be in the same sector as your target using a jump inhibitor, as you know active jump inhibitors will alert affected pilots they are being inhibited so either way you completely kill you element of surprise before you are even able to start thinking about damage to a target and being within knife fighting range of a target ruins the point of even using missiles, you are better off using a cannon or a beam in these scenarios, they are much more effective in these scenarios, using a cannon or beam in a stealth attack is makes no fucking sense whatsoever, I have never heard of a main battle tank sneaking up on another main battle tank to use its .50 cal machinegun on it, it should be common sense that using the longer ranged cannon on the tank is much more effective than sneaking up to use a .50 cal machinegun.
Also worth mentioning that in order to have any effective weapon on a stealth ship you can only jam, cloaking is not possible if you want your stealth ship to have any capability of doing damage.
Now one common theme I am seeing in this missile nerf thread is that missiles are a sniper type weapon and that is bad, missiles being a sniper weapon is NOT A BAD THING.
A typical sniper in a real life scenario is going to sit at a vantage point a long distance away picking off targets at long range with a high damage low rate of fire weapon with a long reload time, the same can be said about missiles in StarMade which have similar characteristics to a standard marksman or sniper rifle.
A sniper is not invincible! once a sniper is spotted they are very easy to take out, the easiest way to take out a sniper is to take the advantage of their range away from them, the most common way to do this is to flank a sniper from a direction they are not watching and engage in CQC against said sniper, a sniper cannot win in a CQC scenario, the same is true for stealth missile snipers in StarMade, you can quite literally use a jump drive to jump into the sector of a sniper and use an inhibitor and kill them, you do not even need to flank them!
Alerting people that a missile is incoming completely kills long ranged combat, especially stealth combat, long ranges nothing is stopping a target from jumping away and never being seen again as soon as they hear a "BEEP BEEP BEEP BEEP" and the methods to counter this require you to enter knife fighting range, if you have to enter knife fighting range to stop an enemy from jumping away at the first sign on danger then you can forget having the element of surprise!