So I'm not 100% on the exact way you have set this game up, but I seem to have encountered an issue straight out the gate.
I noticed that you can get bone from digging dirt. Doing so does produce a bone after a while, but in doing so the dirt is not returned. If that's intended, the recipe should be updated. If it isn't, that's where the initial issue is.
You can place a sappling on any block, so I figured that if the recipe was just incorrect maybe using bonemeal on the sappling when it's placed on any block would then allow progressing and you could make dirt later, but upon using both of the resulting bonemeal a sound is played and the sappling vanishes, but no tree grows. This effectively makes you unable to do anything else in the game. I know that trees do grow on their own, but I figured you'd put in some way to not have to wait for up to an hour to continue playing. I tested this over multiple worlds as it only takes a few minutes to make a new one and get to that point again, and each time it results in the same thing. No mods are loaded that didn't come with the game itself.
So I'm not 100% on the exact way you have set this game up, but I seem to have encountered an issue straight out the gate.
I noticed that you can get bone from digging dirt. Doing so does produce a bone after a while, but in doing so the dirt is not returned. If that's intended, the recipe should be updated. If it isn't, that's where the initial issue is. You can place a sappling on any block, so I figured that if the recipe was just incorrect maybe using bonemeal on the sappling when it's placed on any block would then allow progressing and you could make dirt later, but upon using both of the resulting bonemeal a sound is played and the sappling vanishes, but no tree grows. This effectively makes you unable to do anything else in the game. I know that trees do grow on their own, but I figured you'd put in some way to not have to wait for up to an hour to continue playing. I tested this over multiple worlds as it only takes a few minutes to make a new one and get to that point again, and each time it results in the same thing. No mods are loaded that didn't come with the game itself.