Tip: Layer 3 backgrounds and tides disappear when you hit a message box, so plan your level around that. For example, you can add a sublevel without layer 3 at the start/midpoint, and include your message there.
There are currently no overworld sprites hosted in the section, so the desire for them is rather small. I think that's why the project is going slowly. Anyhow, it also means it's not the highest priority. All of this will get sorted out eventually, but do keep in mind that this is just a hobby for everyone involved - real life comes first.
Yeah, we don't even have a propper and standardized overworld sprite tool replacement and this one isn't receiving support, that seems just fine lol.
Well, I found what was the problem and fixed it by changing some code in the source file and compiled it again using DevCPP. It's not patching the same thing multiple times anymore, now it correctly checks if the patch was applied to the ROM and finds the correct bank number. If anyone is interested in having the fixed version, PM me.
I doubt this tool is likely to receive much support. It's been deprecated for a while and there is currently ongoing discussion (snrk) about the future handling of overworld sprites. When (and if) people show interest in the discussion, this tool will be completely obsolete.
This tool doesn't autoclean itself when inserting new sprites, meaning everytime you use it, it will eat another entire bank from the ROM. It needs to be fixed (although I doubt this tool will ever see any update from now on).