cracks knuckles finally a place I get to share my useless knowledge.
I play with a couple of friends - we have 3 big rules that are largely unspoken
Scrubbles' unofficial multiplayer "Rules"
Please remember this is just what my friend group has decided, there are no "right" or "wrong" ways to play Satisfactory, play however you prefer!
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No clipping. This is a group decision, but we feel that it's more challenging and looks better if we force ourselves not to clip. (or at least avoid it at all costs). Builds are bigger, more complex, and it comes out looking nice
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Build buildings. Cover up your builds. Group builds will get huge and there is a performance hit if you have all of your buildings out in the open. This doesn't really matter until Tier 3 or so, but after that yeah it's pretty important. (Our Gold Coast oil production can span the entire coast, and the game will have to show all of that if you don't build some nice buildings. Also it just looks pretty cool if you put some thought into it.
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This is the big one you talked about and you just have to go over it. There are no good rules for "Don't touch my stuff" as all groups are different, but we have a good baseline of
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If you want to take on a build - then awesome you should feel all empowered to do so. No one should come in and change your build, of course unless asked
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HOWEVER - we all play at a different pace. We like to joke that this isn't work... but at the same time if you say you're going to produce 100 steel beams/min, I'm going to build my build based on those numbers. We have a pseudo AFK rule, if you leave the game and don't give a good time of when the build will be finished, there are no hurt feelings if someone else jumps in and finishes it for you. It was there for you, you chose not to log in one day, and that's going to have to be okay.
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Edit - Also another unspoken exception we have, if you fuck something up, get the math wrong, or our favorite where sometimes conveyors/pipes don't "stitch" together there are no hurt feelings if someone comes in and fixes it.
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I can play 16 hours in a day when I'm really into it. Other folks may not log in once that day, it's just a thing we have to talk about and understand. I don't expect them to be logged in 16 hours a day with me to finish their build, but if they're AFK for a couple of days and I need it... well, yeah I may go finish it.
Rail Network
Those are the only "rules" we have. As for a rail system, I'd recommend personally that someone "takes charge" in planning rail and hooking up factories. Someone who has the entire network in their head on how things are moving. Everyone should be welcome to help, but rail networks get complicated fast and it's good to have a point (wo)man.
A good way to help organize this I've found is to make a "Departures Board" of all of your trains, especially at hubs, so make any sense out of what is happening.
Just like the real ones
You too can put some up that explains where resources are going in or out.
Hub
Finally, make transportation and the Hub a big focal point. Make it fun. For our last build we made the Hub separate from our main construction, and moved all of our train hubs there. That also made it perfect for building our warehouse, and on top of that we put the center of our hypertube network. Make it a fun place to stop in, and make it easy to craft new gear there if you get stranded. This is especially important in multiplayer so your friends aren't going "Where the hell did Scrubbles put the chest of Encased Steel Beams?!"
Also, make a good todo board, so everyone knows what everyone is doing. Try to make it easy and clean to understand. We chose this format
It keeps everyone aware of what people are working on and cuts down on duplicated effort.
Server Maintenance
Your factory server will crash. It just will. Once our factory got large enough in Update 7 it happened probably once a day. Know that someone is going to need to be on call - or you're going to all need access to the server and know how to spin it up if it crashes. Keep backups of the saves in a neutral places anyone can access so if someone accidentally nukes the server you can at least have the saves. (I personally recommend setting up rclone or something to sync your saves somewhere like google drive)
Summing up
Finally, always find ways to keep morale up. Ficsit demands morale be just high enough to remain productive. Give helpful reminders to your friends whenever possible.
That's all I have! Have fun on your next factory, and remember, remain efficient.