account for extensions indirectly depending on each other in parallel package precompilation (#53972)

In the parallel package precompilation code we are mapping what packages
depend on what other packages so that we precompile things in the
correct order ("bottom up") and so what we can also detect cycles and
avoid precompiling packages in those cycles. However, we fail to detect
one type of dependency which is that an extension can "indirectly"
depend on another extension. This happens when the transitive
dependencies of the extension (it's parent + triggers) are a superset of
the dependencies of another extension. In other words, this means that
the other extension will get loaded into the first extension once it
gets loaded, effectively being a dependency.

The failure to model this leads to some issues, for example using one of
the examples in our own tests:

```julia
julia> Base.active_project()
"/home/kc/julia/test/project/Extensions/HasDepWithExtensions.jl/Project.toml"

(HasDepWithExtensions) pkg> status --extensions
Project HasDepWithExtensions v0.1.0
Status `~/julia/test/project/Extensions/HasDepWithExtensions.jl/Project.toml`
  [4d3288b3] HasExtensions v0.1.0 `../HasExtensions.jl`
              ├─ ExtensionFolder [ExtDep, ExtDep2]
              ├─ Extension [ExtDep]
              └─ LinearAlgebraExt [LinearAlgebra]

julia> Base.Precompilation.precompilepkgs(; timing=true)
Precompiling all packages...
    196.1 ms  ✓ HasExtensions
    244.4 ms  ✓ ExtDep2
    207.9 ms  ✓ SomePackage
    201.6 ms  ✓ ExtDep
    462.5 ms  ✓ HasExtensions → ExtensionFolder
    200.1 ms  ✓ HasExtensions → Extension
    173.1 ms  ✓ HasExtensions → LinearAlgebraExt
    222.2 ms  ✓ HasDepWithExtensions
  8 dependencies successfully precompiled in 2 seconds

julia> Base.Precompilation.precompilepkgs(; timing=true)
Precompiling all packages...
    213.4 ms  ✓ HasExtensions → ExtensionFolder
  1 dependency successfully precompiled in 0 seconds. 7 already precompiled.

julia> Base.Precompilation.precompilepkgs(; timing=true)

julia>
```

We can see here that `ExtensionFolder` gets precompiled twice which is
due to `Extension` actually being an "indirect dependency" of
`ExtensionFolder` and therefore should be precompiled before it.

With this PR we instead get:

```julia
julia> Precompilation.precompilepkgs(; timing=true)
Precompiling all packages...
    347.5 ms  ✓ ExtDep2
    294.0 ms  ✓ SomePackage
    293.2 ms  ✓ HasExtensions
    216.5 ms  ✓ HasExtensions → LinearAlgebraExt
    554.9 ms  ✓ ExtDep
    580.9 ms  ✓ HasExtensions → Extension
    593.8 ms  ✓ HasExtensions → ExtensionFolder
    261.3 ms  ✓ HasDepWithExtensions
  8 dependencies successfully precompiled in 2 seconds

julia> Precompilation.precompilepkgs(; timing=true)

julia>
```

`Extension` is precompiled after `ExtensionFolder` and nothing happens
on the second call.

Also, with this PR we get for the issue in
#53081 (comment):

```julia
(jl_zuuRGt) pkg> st
Status `/private/var/folders/tp/2p4x9ygx48sgsdl1ccg1mp_40000gn/T/jl_zuuRGt/Project.toml`
⌃ [d236fae5] PreallocationTools v0.4.17
⌃ [0c5d862f] Symbolics v5.16.1
Info Packages marked with ⌃ have new versions available and may be upgradable.

julia> Precompilation.precompilepkgs(; timing=true)
┌ Warning: Circular dependency detected. Precompilation will be skipped for:
│   SymbolicsPreallocationToolsExt
│   SymbolicsForwardDiffExt
```

and we avoid precompiling the problematic extensions.

This should also allow extensions to precompile in parallel which I
think was prevented before (from the code that is removed in the
beginning of the diff).

(cherry picked from commit df89440)

Author: KristofferC

base/precompilation.jl

@@ -399,7 +399,6 @@ function precompilepkgs(pkgs::Vector{String}=String[];
         depsmap[pkg] = filter!(!Base.in_sysimage, deps)
         # add any extensions
         pkg_exts = Dict{Base.PkgId, Vector{Base.PkgId}}()
-        prev_ext = nothing
         for (ext_name, extdep_uuids) in env.extensions[dep]
             ext_deps = Base.PkgId[]
             push!(ext_deps, pkg) # depends on parent package
@@ -414,13 +413,8 @@ function precompilepkgs(pkgs::Vector{String}=String[];
                 end
             end
             all_extdeps_available || continue
-            if prev_ext isa Base.PkgId
-                # also make the exts depend on eachother sequentially to avoid race
-                push!(ext_deps, prev_ext)
-            end
             ext_uuid = Base.uuid5(pkg.uuid, ext_name)
             ext = Base.PkgId(ext_uuid, ext_name)
-            prev_ext = ext
             filter!(!Base.in_sysimage, ext_deps)
             depsmap[ext] = ext_deps
             exts[ext] = pkg.name
@@ -431,6 +425,51 @@ function precompilepkgs(pkgs::Vector{String}=String[];
         end
     end
 
+    # An extension effectively depends on another extension if it has all the the
+    # dependencies of that other extension
+    function expand_dependencies(depsmap)
+        function visit!(visited, node, all_deps)
+            if node in visited
+                return
+            end
+            push!(visited, node)
+            for dep in get(Set{Base.PkgId}, depsmap, node)
+                if !(dep in all_deps)
+                    push!(all_deps, dep)
+                    visit!(visited, dep, all_deps)
+                end
+            end
+        end
+
+        depsmap_transitive = Dict{Base.PkgId, Set{Base.PkgId}}()
+        for package in keys(depsmap)
+            # Initialize a set to keep track of all dependencies for 'package'
+            all_deps = Set{Base.PkgId}()
+            visited = Set{Base.PkgId}()
+            visit!(visited, package, all_deps)
+            # Update depsmap with the complete set of dependencies for 'package'
+            depsmap_transitive[package] = all_deps
+        end
+        return depsmap_transitive
+    end
+
+    depsmap_transitive = expand_dependencies(depsmap)
+
+    for (_, extensions_1) in pkg_exts_map
+        for extension_1 in extensions_1
+            deps_ext_1 = depsmap_transitive[extension_1]
+            for (_, extensions_2) in pkg_exts_map
+                for extension_2 in extensions_2
+                    extension_1 == extension_2 && continue
+                    deps_ext_2 = depsmap_transitive[extension_2]
+                    if issubset(deps_ext_2, deps_ext_1)
+                        push!(depsmap[extension_1], extension_2)
+                    end
+                end
+            end
+        end
+    end
+
     @debug "precompile: deps collected"
     # this loop must be run after the full depsmap has been populated
     for (pkg, pkg_exts) in pkg_exts_map
@@ -739,6 +778,7 @@ function precompilepkgs(pkgs::Vector{String}=String[];
     end
     @debug "precompile: starting precompilation loop" depsmap direct_deps
     ## precompilation loop
+
     for (pkg, deps) in depsmap
         cachepaths = Base.find_all_in_cache_path(pkg)
         sourcepath = Base.locate_package(pkg)
@@ -811,6 +851,7 @@ function precompilepkgs(pkgs::Vector{String}=String[];
                             end
                             loaded && (n_loaded += 1)
                         catch err
+                            # @show err
                             close(std_pipe.in) # close pipe to end the std output monitor
                             wait(t_monitor)
                             if err isa ErrorException || (err isa ArgumentError && startswith(err.msg, "Invalid header in cache file"))
@@ -834,7 +875,8 @@ function precompilepkgs(pkgs::Vector{String}=String[];
                     notify(was_processed[pkg_config])
                 catch err_outer
                     # For debugging:
-                    # println("Task failed $err_outer") # logging doesn't show here
+                    # println("Task failed $err_outer")
+                    # Base.display_error(ErrorException(""), Base.catch_backtrace())# logging doesn't show here
                     handle_interrupt(err_outer) || rethrow()
                     notify(was_processed[pkg_config])
                 finally