Precompiling broken when no manifest

Precompiling broken when no manifest 

I broke this in https://github.com/JuliaLang/julia/pull/59122

I'm surprised CI didn't catch this.. evidently needs a test.


```
% julia +nightly --project=../Pkg.jl -ie "using Pkg, REPL"
ERROR: KeyError: key Base.PkgId(Base.UUID("fa267f1f-6049-4f14-aa54-33bafae1ed76"), "TOML") not found
```