Make loading work when stdlib deps are missing in the manifest (JuliaLang#56148)

Closes JuliaLang#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
...
```

Author: IanButterworth

base/loading.jl

@@ -308,6 +308,21 @@ function find_package(arg) # ::Union{Nothing,String}
     return locate_package(pkg, env)
 end
 
+# is there a better/faster ground truth?
+function is_stdlib(pkgid::PkgId)
+    pkgid.name in readdir(Sys.STDLIB) || return false
+    stdlib_root = joinpath(Sys.STDLIB, pkgid.name)
+    project_file = locate_project_file(stdlib_root)
+    if project_file isa String
+        d = parsed_toml(project_file)
+        uuid = get(d, "uuid", nothing)
+        if uuid !== nothing
+            return UUID(uuid) == pkgid.uuid
+        end
+    end
+    return false
+end
+
 """
     Base.identify_package_env(name::String)::Union{Tuple{PkgId, String}, Nothing}
     Base.identify_package_env(where::Union{Module,PkgId}, name::String)::Union{Tuple{PkgId, Union{String, Nothing}}, Nothing}
@@ -336,6 +351,12 @@ function identify_package_env(where::PkgId, name::String)
             end
             break # found in implicit environment--return "not found"
         end
+        if pkg_env === nothing && is_stdlib(where)
+            # if not found it could be that manifests are from a different julia version/commit
+            # where stdlib dependencies have changed, so look up deps based on the stdlib Project.toml
+            # as a fallback
+            pkg_env = identify_stdlib_project_dep(where, name)
+        end
     end
     if cache !== nothing
         cache.identified_where[(where, name)] = pkg_env
@@ -362,6 +383,22 @@ function identify_package_env(name::String)
     return pkg_env
 end
 
+function identify_stdlib_project_dep(stdlib::PkgId, depname::String)
+    @debug """
+    Stdlib $(repr("text/plain", stdlib)) is trying to load `$depname`
+    which is not listed as a dep in the load path manifests, so resorting to search
+    in the stdlib Project.tomls for true deps"""
+    stdlib_projfile = locate_project_file(joinpath(Sys.STDLIB, stdlib.name))
+    stdlib_projfile === nothing && return nothing
+    found = explicit_project_deps_get(stdlib_projfile, depname)
+    if found !== nothing
+        @debug "$(repr("text/plain", stdlib)) indeed depends on $depname in project $stdlib_projfile"
+        pkgid = PkgId(found, depname)
+        return pkgid, stdlib_projfile
+    end
+    return nothing
+end
+
 _nothing_or_first(x) = x === nothing ? nothing : first(x)
 
 """

test/loading.jl

@@ -1341,6 +1341,18 @@ end
     end
 end
 
+@testset "Fallback for stdlib deps if manifest deps aren't found" begin
+    mktempdir() do depot
+        # This manifest has a LibGit2 entry that is missing LibGit2_jll, which should be
+        # handled by falling back to the stdlib Project.toml for dependency truth.
+        badmanifest_test_dir = joinpath(@__DIR__, "project", "deps", "BadStdlibDeps.jl")
+        @test success(addenv(
+            `$(Base.julia_cmd()) --project=$badmanifest_test_dir --startup-file=no -e 'using LibGit2'`,
+            "JULIA_DEPOT_PATH" => depot * Base.Filesystem.pathsep(),
+        ))
+    end
+end
+
 @testset "code coverage disabled during precompilation" begin
     mktempdir() do depot
         cov_test_dir = joinpath(@__DIR__, "project", "deps", "CovTest.jl")

test/project/deps/BadStdlibDeps/Manifest.toml

@@ -0,0 +1,51 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.12.0-DEV"
+manifest_format = "2.0"
+project_hash = "dc9d33b0ee13d9466bdb75b8d375808a534a79ec"
+
+[[deps.Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.11.0"
+
+# This is intentionally missing LibGit2_jll for testing purposes
+[[deps.LibGit2]]
+deps = ["NetworkOptions", "Printf", "SHA"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+version = "1.11.0"
+
+[[deps.LibGit2_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
+uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
+version = "1.8.0+0"
+
+[[deps.LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.11.0+1"
+
+[[deps.Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+version = "1.11.0"
+
+[[deps.MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.6+1"
+
+[[deps.NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
+
+[[deps.Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+version = "1.11.0"
+
+[[deps.SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
+
+[[deps.Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+version = "1.11.0"

test/project/deps/BadStdlibDeps/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"