One very helpful thing is to look at your error log after loading up a game, which you can find in
/Documents/Paradox Interactive/Stellaris/logs/error.log
If you don't have my Venture Politics mod downloaded/enabled, you will see something like this:
"[17:30:06][trigger_impl.cpp:8520]: has_district trigger uses inexistent district: district_arcology_trade. file: common/deposits/exodus_mod_deposits.txt line: 122"

If you see that line, the mod is loading in. If you see other stuff flagging files that have "exodus_mod" in the name, that is the most valuable to tell me about.

In case you see some of the blockers or features spawn in your non homeworld planets, (I believe it's been fixed with the latest update but you never know)
you can use the console command effect = {remove_deposit = KEY} while looking at that planet's planet screen using the folowwing keys:
d_hydroponic_arcology
d_overloaded_infrastructure (weather controkl tech blocker)
d_overloaded_infrastructure_2 (antigrav tech blocker)
d_overloaded_infrastructure_3 (decrepit urban corridor)
d_dwindling_stockpile
d_plentiful_stockpile
d_renewed_city (peerless megalopolis)

The thing with the blockers spawning in non-homeworld planets still persists, but have only encountered d_overloaded_infrastructure_2. Seems like it's missing:

Thanks for catching that. I'll fix it momentarily (and remove the tech locked blockers from showing on the tech screen, since it's a bit annoying when you aren't playing that origin.)

Hello. I was wondering if having Ecumenopolis's spawn near your home system was intentional or something that can't really be helped? I am guessing that since technically they are your species preferred planet class that the game spawns them in place of say, a continental planet which would be nice to have instead. Just wanted to let you know. Didn't see anyone else mention it so I thought I should.

That behavior is not caused by this mod, but one of my friends plays with a bunch of mods and reported that same thing (which went away when he disabled a bunch of them, I don't use his modlist, so I'm not certain what it was.)

The way this mod works is your homeworld is actually generated as a regular, default homeworld - I don't modify map generation at all. Then, after all the map generation stuff, this mod fires and clears your homeworld of features, sets it to an ecumenopolis, and adds what it needs.

However, because lots of mods use this same "start of game event" trigger, what's probably happening is there is a mod that is trying to setup matching worlds, but it's grabbing your capital's planet_class (which has now been set to pc_city) instead of your species climate preference.

Notice that this mod doesn't result in your species getting Ecumenopolis preference - you keep whatever you chose at startup. I just rolled a random map to verify that I get the correct planet classes (continental in my case) for my guaranteed colonies.

I did notice that my preference was continental when I tested it out last night. I will check my mods as well. I will let you know what mod was causing it for reference when and if I find out. Btw, the way you made the Ecumenopolis the starting planet is very clever. Thank you for responding so quickly and with great detail. I love your mod so far btw.

Also, I am using Sol system Expanded 25 tile earth as my system. Don't know if that would cause issues. I recently noticed that particular version of the mod hadn't been updated in a while. Will check though.

So I found that Sol System Expanded is causing this issue. Whether its the updated version or the out of date 25 tile Earth version. It is what is causing this issue. I haven't looked at the code, and it probably would take me a bit to understand what it means, though I have some experience with what different lines of coding mean. (I took a computer programming class in High school in 2018; Yes I know this isn't much experience at all) What I am guessing is happening here is that the Sol System Expanded mod likely sets the guaranteed habitable planets based on the type of planet your capital is rather than preference. I noticed this issue when I first played the Federation DLC when I played the start in which you planet is a relic world. I also noticed it when playing with a tomb world a year ago. Both times, I assumed it was a fault on paradox though I was not certain so I didn't rush to conclusions. However, both times I had been using Sol System Expanded. What I did to confirm was to start a game with Sol System Expanded as my home system and then type intel in console to reveal the planets near me while using your origin. Every time I did so, the planets were Ecumenopolis's. Then I tried the same thing but with default Sol while having Sol System Expanded installed. Those planets were also Ecumenopolis's. Then I continued to try the same thing with SSE installed but on different systems; I did the random spawn, and Deneb. All with the same outcome as before. Then I deactivated the SSE mod and tried the same tests. The worlds were now continental as they should be. I then reactivated the mod and did the same tests again to confirm, with the same outcome as I had originally. I then deactivated it and then installed the updated version. That version also had the same issue.

So I can confirm that it is that mod and not yours. I will see if I can report this issue on that mod's bug report page.

Ran into an issue with the planetary rebuilding. Colonised a second world, got the flag for stuff expanding and whatnot, but the following flag to give me the option to research the +1 Housing tech didn't fire off. Ended up getting it the hard way and fixing up my homeworld, but nothing else fired off and I was stuck with an underdeveloped world. Also, the Special Project didn't show up, nor did a decision in the planetary menu.

Not sure if it's a mod conflict somewhere (only added three mods since installing - the Espionage one, the expanded list mod it has as a requirement and a patch to make it appear on the expanded UI. Mod worked with everything else) or just a bug/glitch. Ended up doing the event skip cheat to flag it as finished.

@Ghost333 I have been looking at this, apologies for being a little behind in replying.
So what's supposed to happen is once you begin colonizing a new planet for the first time, a timer of 1850 days is started. This is event exodus.31. 1850 is to have the second part, exodus.32, trigger just after the setup is done and you have a new colony "officially" going.

However, exodus.32 immediately triggers exodus.25, which is what grants the special project.
So quite literally once your colony ships touches down you should be on a timer to get the special project; there is no condition to prevent it from happening. I have never been able to actually break the sequence myself.

Upon completing the project, event exodus.26 is triggered. So if, for whatever reason, this is happening to you over and over, you can type exodus.25 to grant the project; if that's no dice, exodus.26 is the project outcome and you can trigger that to mitigate using the entire skip event.
If its persistent I have to think something strange is going on for you that is somehow blocking special projects. It's not very elaborate code.

I got a bug where colonizing a planet shows the meteoric colony ship's landing sequence, and also gives 150 engineering. The modifier isn't applied thankfully, but it's a small bug.

Is this mod intended to remove guaranteed habitable worlds, or is it just conflicting with Planetary Diversity?

Also, the climate description is missing in the homeworld select screen.

@Ragnarok
It's probably a conflict with PD. There's no change to the game start scripts. The homeworld setup is done after the galaxy is generated.
My guess is that PD struggles because in order to display the ecumenopolis in the game setup screen, the best solution I can come up with is a bit of a hack to use a placeholder planet class. Otherwise, the image will be partially black because of how paradox has coded the setup screen backgrounds.

Not sure if this is helpful or not since you're already working on updating it for 3.0, but one bug I noticed just playing with it last night was that the severe rationing modifier didn't go away after colonizing nearby worlds and building energy & mining districts on it. I'm fairly certain those modifiers are supposed to go away after colonization, so I think that may be a bug of the 3.0 patch.

There may be various bugs introduced by 3.0 especially with the fact that they changed the game setup script; I've been working on my megacorp mod (which has a much larger file base) before this one.

Once you colonize a new planet, what should happen is a special project will appear in the situation log. (A notification pops up saying your leader has assembled the brightest minds etc.) You complete that project - that enables a planet decision called "Rebuild Ecumenopolis." This decision only appears if you finish the project, and you need the "Weather control systems" tech to take it. Fortunately, the special project gives you a random amount of progress on that tech.

When the "Rebuild" decision finishes, you get showered in rewards.