precompilepkgs: package in boths deps and weakdeps are in fact only weak (#53649)

Missed when porting from Pkg. Fixes
JuliaLang/Pkg.jl#3834.

Author: KristofferC

base/precompilation.jl

@@ -26,6 +26,9 @@ struct ExplicitEnv
 end
 
 function ExplicitEnv(envpath::String=Base.active_project())
+    if !isfile(envpath)
+        error("expected a project file at $(repr(envpath))")
+    end
     envpath = abspath(envpath)
     project_d = parsed_toml(envpath)
 
@@ -51,6 +54,11 @@ function ExplicitEnv(envpath::String=Base.active_project())
         end
     end
 
+    # A package in both deps and weakdeps is in fact only a weakdep
+    for (name, _) in project_weakdeps
+        delete!(project_deps, name)
+    end
+
     project_extensions = Dict{String, Vector{UUID}}()
     # Collect all extensions of the project
     for (name, triggers::Union{String, Vector{String}}) in get(Dict{String, Any}, project_d, "extensions")::Dict{String, Any}