Fix historical stdlib fixup if Pkg is in the Manifest

[Keno]

The code here appeared to be untested and broke whenever something actually used it. Example backtrace:

julia> JLLPrefixes.collect_artifact_paths(["ripgrep_jll"])
ERROR: MethodError: no method matching haskey(::Vector{Base.UUID}, ::String)
The function `haskey` exists, but no method is defined for this combination of argument types.

Closest candidates are:
  haskey(::Pkg.Types.Manifest, ::Any)
   @ Pkg ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/Pkg/src/Types.jl:323
  haskey(::REPL.Terminals.TTYTerminal, ::Any)
   @ REPL ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/REPL/src/Terminals.jl:155
  haskey(::LibGit2.CachedCredentials, ::Any)
   @ LibGit2 ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/LibGit2/src/types.jl:1357
  ...

Stacktrace:
  [1] fixups_from_projectfile!(ctx::Pkg.Types.Context)
    @ Pkg.Operations ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:238
  [2] add(ctx::Pkg.Types.Context, pkgs::Vector{…}, new_git::Set{…}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
    @ Pkg.Operations ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1710
  [3] add
    @ ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1680 [inlined]
  [4] add(ctx::Pkg.Types.Context, pkgs::Vector{…}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{…})
    @ Pkg.API ~/.julia/juliaup/julia-nightly/share/julia/stdlib/v1.13/Pkg/src/API.jl:328