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They never removed it as it was never a feature in the first place (I think, I played since ver 3 and have never seen a tree leave behind a hole). I would suggest that you automate tree farming by having a few bots doing these jobs.

-Digging holes

-Planting

-Chopping

-Logs/Seed collection

It's really a way to combat a fairly common graphic bug where the hover info never disappeared. Maybe when the game is further developed or is requested enough times, then a new UI may be implemented or the old one would be restored.

Dig them up using a shovel.

Weird graphical issue. If a bot has a script and you put in a new script using the floppy disk, the old script is visible underneath it.

This is a bug that the devs have known about, and are unable to replicate. Try using a different computer.

That isn't night. Day/night cycles haven't been implemented. What you're seeing is a bug that the devs haven't been able to replicate, making it harder to fix.

The hoe is used on soil (just soil, not tree soil). A wiki has been created; check the discord server for the link. Press e and hit the delete button on pc or fn and backspace on mac. Stone as of now has no other use besides crude tools and as building materials.

Simply delete the storage and place it down again.  Open your build menu and hit the delete key on PC or fn and backspace on mac. 

It's a known bug and it may be fixed whenever version 6 is out.

Basic gears require a wood router to be made. Metal gears currently have no use.

The gates probably think that the other gate is a solid block ie a fence. Might be a bug or it hasn't been implemented into the game yet.

With mushrooms use a shovel. For weeds dig them up and use fertilizer on them. Get fertilizer by taking dung and putting it into fertilizer storage (it auto-converts the dung into fertilizer). For bushes I have no clue, might be good idea to ask on discord, it's quicker and the devs and any other player can answer must more quickly.

Might just be your script. Try changing it to be similar to the one in the image. 

The general storage is used to store the tools.

There is no way to move buildings once they've been built, but there is a way to move them. Open your build menu (hit e) and press either the delete key (don't hit backspace) on pc or fn+backspace on mac. 

Any building that have been deleted are saved and are built instantly the next time you place its blueprint down.

Hit r to rotate blueprints.

A quick recommendation; There should be a way to get rid of any unwanted or excess materials. 

Also, this game is incredibly satisfying once players begin to automate.

Possible bug (or me being dumb) Can't seem to delete the metal crafting bench.