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Make loading work when stdlib deps are missing in the manifest (#56148)
Closes#56109
Simulating a bad manifest by having `LibGit2_jll` missing as a dep of
`LibGit2` in my default env, say because the manifest was generated by a
different julia version or different master julia commit.
## This PR, it just works
```
julia> using Revise
julia>
```
i.e.
```
% JULIA_DEBUG=loading ./julia --startup-file=no
julia> using Revise
...
┌ Debug: Stdlib LibGit2 [76f85450-5226-5b5a-8eaa-529ad045b433] is trying to load `LibGit2_jll`
│ which is not listed as a dep in the load path manifests, so resorting to search
│ in the stdlib Project.tomls for true deps
└ @ Base loading.jl:387
┌ Debug: LibGit2 [76f85450-5226-5b5a-8eaa-529ad045b433] indeed depends on LibGit2_jll in project /Users/ian/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/LibGit2/Project.toml
└ @ Base loading.jl:395
...
julia>
```
## Master
```
julia> using Revise
Info Given Revise was explicitly requested, output will be shown live
ERROR: LoadError: ArgumentError: Package LibGit2 does not have LibGit2_jll in its dependencies:
- Note that the following manifests in the load path were resolved with a potentially
different DEV version of the current version, which may be the cause of the error.
Try to re-resolve them in the current version, or consider deleting them if that fails:
/Users/ian/.julia/environments/v1.12/Manifest.toml
- You may have a partially installed environment. Try `Pkg.instantiate()`
to ensure all packages in the environment are installed.
- Or, if you have LibGit2 checked out for development and have
added LibGit2_jll as a dependency but haven't updated your primary
environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with LibGit2
...
```
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