Anyone with invisible items in-hand and items being too small in-game (in need of scaling) please read this:
I have spent the last absurd amount of hours trying to figure out these two issues (more so the invisible item part), and I have found what worked for me, assuming you have your .lua files typed accordingly and you compile the two animation files with the proper names (yourmod - idle and yourmod - BUILD). I had all the assets listed, no "errors" in the pre-game compile in CMD, and the inventory and ground animations I could see just fine.
Thanks to Cheerio and his example item mod, I was able to properly rule out the file system layout. I followed the OP's file layout, and everyone else's supposed "correct" layout they had responded to other people with the same issue's question to and had no luck in resolving this issue. To have no invisible item in-hand, copy his EXACT file layout. Do not worry about the .zip files for they will be compiled automatically.
The PROPER mod file system layout for Don't Starve: Together is the following:
This is for the ground animation (your item just sitting on the ground.)
yourmod > exported > yourmod (contains yourmod.scml) > yourmod > yourmod.png
This is for the in-hand animation (your item being held by a player.)
yourmod > exported > swap_yourmod (contains swap_yourmod.scml) > yourmod > yourmod.png
This is for the inventory icon (your item in your inventory.)
yourmod > images > inventoryimages > yourmod.png
If this does not resolve the issue for you, then I simply advise to triple check your .lua files and .scml data.
As for the item being scaled too small, simply change the resolution of the .png files used for the compiling. I found that these sizes worked perfectly for me:
Inventory icon - 64 x 64
Item on ground - 200 x 200
Item in-hand - 200 x 200
I really hope this helps someone. This process was very painful and honestly should have been updated for 2019 by at least one person by now. The method listed by the OP still works of course, but it is definitely outdated and unclear in specific areas. Thanks again ,OP! I guess as the game updated some of the old layouts needed updating.
(That wasn't supposed to sound hostile lol I'm genuinely thankful for your post, I couldn't have done anything with out it :D)