Add -isystem ${includedir} for clang on FreeBSD, and GCC on musl (#226)

* Add `-isystem ${includedir}` for clang on FreeBSD, and GCC on musl

Currently several JLLs need to manually add `-I${includedir}` to their
CPPFLAGS in order to build correctly on these platforms. Fix this by
adjusting the compiler wrappers.

See JuliaPackaging/Yggdrasil#3949

Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

Author: fingolfin

src/Runner.jl

@@ -331,6 +331,23 @@ function generate_compiler_wrappers!(platform::AbstractPlatform; bin_path::Abstr
         return "-mmacosx-version-min=$(macos_version(p))"
     end
 
+    function add_system_includedir(flags::Vector{String})
+        # GCC 4.8.5 for musl and clang on FreeBSD do not have `SYSROOT/usr/local` (which
+        # in our build environments is a symlink to $includedir = "$(prefix)/include")
+        # in the default list of include search directories. As a result, quite some
+        # builders that work fine everywhere else need to add something like
+        # `-I${includedir}` to their CPPFLAGS.
+        #
+        # To remove this annoyance, we simply add it here. We use `-isystem` instead
+        # of `-I` to mimic how this dir is treated on other operating systems. It
+        # is still not a perfect match, as the order of the default search directories
+        # differs, but this should not matter in practice.
+        #
+        # See also https://github.com/JuliaPackaging/Yggdrasil/issues/3949 and
+        # https://github.com/JuliaPackaging/Yggdrasil/pull/3969 for further details.
+        append!(flags, ["-isystem", raw"${includedir}"])
+    end
+
     function clang_compile_flags!(p::AbstractPlatform, flags::Vector{String} = String[])
         if lock_microarchitecture
             append!(flags, get_march_flags(arch(p), march(p), "clang"))
@@ -351,6 +368,9 @@ function generate_compiler_wrappers!(platform::AbstractPlatform; bin_path::Abstr
                 min_macos_version_flag(p),
             ])
         end
+        if Sys.isfreebsd(p)
+            add_system_includedir(flags)
+        end
         return flags
     end
 
@@ -420,6 +440,10 @@ function generate_compiler_wrappers!(platform::AbstractPlatform; bin_path::Abstr
         if lock_microarchitecture
             append!(flags, get_march_flags(arch(p), march(p), "gcc"))
         end
+        gcc_version, llvm_version = select_compiler_versions(p, compilers)
+        if libc(platform) == "musl" && gcc_version in (v"4.8.5", v"5.2.0")
+            add_system_includedir(flags)
+        end
         return flags
     end