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The most basic advice routinely parroted on the discord goes like this
Intel is far and away the most valuable activity and is always underestimated by new players because the game does a poor job at explaining missions spawning and detection. Rule of thumb:
-always run full intel in active regions
-only ever run supplies in liberated regions (and generally there run exclusively supplies)
-if you ever feel the need to do the recruit activity, put everyone on recruit with a high ranking advisor for rapid returns until you get to the desired number of personel and then switch out entirely to intel (or supply in liberated regions).
-Regions go in hiding (all but 2 personnel in hiding) once the region strength exceed a threshold.
For the new players, its often recommended to shut down regions when STR>4 because STR 5-6 have a baseline activity of 13-15 on missions. But as you progress and maybe go up the difficulty settings that threshold for shutting down regions has to go up, usually to STR>6. The reason for shut down rules of 2 non-hidding is tied to chosen retaliation mechanics described on the wiki https://www.ufopaedia.org/index.php?title=Haven_Management_(LWOTC)#ADVENT_Retaliations
If you fall behind on the strategic layer, there's a soft shutdown that consists of putting 2 intel / 2 supply / 2 recruit which still allows "full retal" missions, but not job-specific retal missions. I wouldn't advise it but its an option.
I play on legend ironman at this point and I almost never switch off intel except to shut down regions, even when I have the maximum number of GOPs missions queued in a region and have my entire barrack deployed, injured or in some training activity. There are a few reasons for this. First, some of the most critical missions in the game that help the player control the global alien strength can still spawn, and will generally spawn in regions where you are most active, and they are not gated behind the "max # simultaneous guerrilla ops" thresholds. Those missions are worth cancelling out another to run them. Second, missions tend to respawn shortly after one is completed and intel ticks at fixed intervals rather than smoothly over time. If you switch back from supplies to intel after you complete a mission to help detect the next one, you may end up missing a full tick of intel, basically delaying mission detection by up to 1 day, either causing you to miss a mission or force a riskier squad.
The critical missions that you can detect above the 3 "regular GOPs" that spawn every cycle, are UFO precursor missions, and supply raid missions. UFOs periodically bring aliens from space down to earth. Basic UFOs add +1 STR in the region where they land, and +1 STR in one adjacent region. So even though they have very high intel gathering requirements and low-ish odds to detect, detecting one is gamechanging on the strategic layer. They also reward some loot, enemy bodies, and provide +1 avenger power. Supply raids are moving troops from an adjacent region to this region and thus intercepting them and beating the mission applies -1 STR to the sending region while preventing the +1 STR coming to the current region.
The above missions is why it is often worthwhile to scan with the avenger in your most active region (scanning with the avenger counts as +4 rebels on intel), and why it can be a meaningful decision to slot a scientist advisor from time to time. The aliens periodically move troops from low vigilance regions towards high vigilance regions, and UFOs are generally sent to regions with high resistance activity (i.e. high vigilance) too.
If as a new player, you chose to shut down your regions when STR>4, I would advise you to set the 2 active personel on intel even though you likely won't run missions in the area. This is beacause another high value mission, the troop column missions, can only spawn in regions with STR>3 (and vigilance <15). These are loot/full salvage(for corpse) missions which reduce the STR in the region by 1. They have pretty low intel requirements to detect, have reduced infiltration time baseline (need 5 days for 5 man instead of 6 days for most GOPs), and running 1 every other month will yield more supplies equivalent value than running 2 guys on supplies for 2 months if you sell loot and harvested bodies.
For very experienced players that pull very far ahead of the aliens (global vigilance >> global strength), the aliens get access to a better version of the UFO missions, called "super UFOs", which if not intercepted, add 2 STR in the region they land, and 1 STR in 2 adjacent regions.
But it is extremely math-y for a forum format.
Now, onto the questions not directly addressed above.
Activities yields are tallied daily, and I believe you get no yields on days you switch jobs but that part I've never been completely sure. The yields have been added to the Haven interface in the 1.2 beta version of the mod. The recruitment yield is a bit difficult to explain, but personel generate 5 intel per day, or 1.2 supply per day, increased by 50% per promotion of the personel (so a double promoted personnel yields as much as 2 unpromoted ones). But the intel yields are difficult to interpret without peeking into the activities.ini file I alluded to.
Anyway, switching everyone to supply for a day before the supply drop could have a net supply yield of 0 if there were no full-days of supply activty, while giving up intel. But even if one full job day ticks, it would still yield relatively small output, generally a lot smaller than the total loot pickup+reward value of running a single extra mission. So its rarely worth unless you have so many regions active (or so many people injured) that you completely overflow with guerrilla ops missions beyond your capacity to run them (and even then I personally still generally value mission reward choices/options above running supply for a short time).
From the start of the game, you should scan your starting region until you detect all missions (2 on legend, 3 otherwise) before you go unlock the black market to improve your first mission cycle timers.
Beyond that, you generally want to scan where you run full intel to add to the intel gathering effort there, but if/when you have 2+ regions running full intel (usually 2 regions on full intel is enough to keep troops constantly busy), out of those regions, you will generally want to scan in areas that can still spawn liberation 1-2-3 missions, or that have very high vigilance where you expect supply raids / UFOs to go to.
Detecting liberation chain missions early and with good timer is probably the highest priority there. So for example, if you have a lib mission which you couldn't take because the timer was too short and such, about 1 day before its timer finishes, I would throw a scientist advisor if I can spare it, and move the avenger in the region to scan it to maximize my odds of detecting the next lib mission spawn with an excellent timer in the region. Can remove the scientist once detected if you are tight on research.
There's a lot of information for me to absorb here, but I think I get the gist of it. I've also been reading a guide on liberation to see how that all ties into this. I got an idea of how to progress now at least. I'm only playing on veteran right now, so I expect there will be more room for mistakes.
I roam around the steam forums but LW subforum is fairly inactive. If you ever struggle to find timely answers on steam, you can try the LWOTC discord. Link should be available on both the mod workshop page and the ufopaedia wiki. It's still fairly active with a lot of old timers doing Q&A for newer players.