Fix precompiling when there's no manifest

[IanButterworth]

Fixes #59206

Here there's no Manifest.toml in the Pkg repo

% ./julia --start=no --project=../Pkg.jl -q -ie "using Pkg, REPL"
Precompiling Pkg finished.
  1 dependency successfully precompiled in 37 seconds
Precompiling REPLExt finished.
  1 dependency successfully precompiled in 5 seconds
julia>

[IanButterworth]

@KristofferC I'd appreciate another set of eyes on this. It's breaking Pkg CI so good to get in quick.

[IanButterworth]

I'll merge as this needs fixing to unblock e.g. Pkg CI, but review still appreciated

[omus]

It appears that this change inadvertently causes the exception LoadError: Unknown package: <pkg-name> to occur if you attempt to precompile an indirect dependency using Pkg.precompile. Noticed on Julia 1.12.1.

[IanButterworth]

I think I was unaware that was possible before... I guess it makes sense.

Mind opening an issue?