This problem with Aqua happens often to me. My best understanding is that Aqua thinks that Pkg.resolve will list the packages in alphabetical order. In particular, if they are not in order running Pkg.resolve again will order them. But in fact this is not the case. Pkg.resolve leaves Project.toml unchanged.
I agree – I was so confused by Aqua’s error message advice to re-run Pkg.resolve(). I had to re-order the packages manually.
Update: PrecompileTools is now considerably more capable than SnoopPrecompile. In addition to several minor improvements, the most significant new feature just came out moments ago in v1.1.0, the addition of @recompile_invalidations which you can read about in the docs.
If you’ve not yet upgraded, now is a great time!
20 Likes