It was done by using CTRL to move facilities around but the feature was removed permanently because I guess it posed no gameplay challenge. I wasn't around back then to fully understand this decision but as a devoted OCD gamer I suffered greatly in its absence. To me there is little challenge in unnecessary delaying the inevitable which ends being optimally placed facilities. But like I said I don't fully understand and some grief is crucial to good gameplay I just don't like the source of it.
Besides functionality my hideouts simply must conform to some aesthetical design (research and leisure close to living which is clumped together, manufacture complex far away bcoz noise, radar in the centre, medical close to living/hangar/prison, storage close to manufacture, and so on lol...). With game constantly throwing new facilitates at you it was impossible to cope in satisfactory way. Just when you thought you placed everything perfectly another one messes up the order. Only in the very end game was I able to finally rest happily when the unknown became known. Couldn't stand to watch YT-ers gameplay videos where they place stuff on first available space, such hideous hideouts.
You aren't the first nor will be the last person to ask but the author is pretty adamant in the feature never again seeing the light of day. What you can do instead is change individual facility coordinates by editing save file. Coords are stored not long after individual hideout names and are relatively straight forward to edit. You gotta weight between immersion break or suffering hehe. I wasn't of the suffering type
I could also showcase you my endgame hideout types with screenshots (or savegame), to help you plan ahead if you wish. 2 research, 4 generic all-in-one, 2 factory/heavy production/income types. Pretty much min/max'd to perfection if I do say so myself. Spoils the living shit out of everything, including your own snese of accomplishment, but that's the price you gotta be willing to pay.
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My suggestion would be to bring back the feature but locked behind mid-game techs. Some shadowrealm ability that lets you teleport matter through their dimension or something, for a price of course (hypno panels? millions? both?. Since the number of facilities only increased since then while hideouts dimensions remain forever fixed some kind of bone thrown in our direction defo wouldn't hurt.
