fix: GCC needs --sysroot for include-fixed, supplement with -isystem

GCC's include-fixed directory contains stdlib.h wrappers that use
#include_next to find the sysroot's stdlib.h. This mechanism only
works with --sysroot, not standalone -isystem paths.

Fix: for GCC, keep --sysroot from probe_sysroot() and supplement
with -isystem for linux kernel headers from payload when the probed
sysroot is missing them. For Clang, continue using --no-default-config
+ explicit -isystem (Clang doesn't have include-fixed).

Author: Sunrisepeak

src/build/flags.cppm

@@ -135,14 +135,25 @@ CompileFlags compute_flags(const BuildPlan& plan) {
         // Linker flags that cfg normally provides
         sysroot_flag += " -fuse-ld=lld --rtlib=compiler-rt --unwindlib=libunwind";
         f.sysroot = sysroot_flag;
+    } else if (!plan.toolchain.sysroot.empty()) {
+        // GCC (or Clang without cfg): use --sysroot from probe.
+        // GCC requires --sysroot for include-fixed headers (stdlib.h wrapper).
+        // Supplement with -isystem for linux kernel headers from payload
+        // if the probed sysroot is missing them.
+        sysroot_flag = " --sysroot=" + escape_path(plan.toolchain.sysroot);
+        if (plan.toolchain.payloadPaths && !plan.toolchain.payloadPaths->linuxInclude.empty()) {
+            auto sysrootLinux = plan.toolchain.sysroot / "usr" / "include" / "linux" / "limits.h";
+            if (!std::filesystem::exists(sysrootLinux))
+                sysroot_flag += " -isystem" + escape_path(plan.toolchain.payloadPaths->linuxInclude);
+        }
+        f.sysroot = sysroot_flag;
     } else if (plan.toolchain.payloadPaths) {
-        // GCC or Clang without cfg: use payload -isystem paths.
+        // No sysroot but have payload paths: use -isystem.
         auto& pp = *plan.toolchain.payloadPaths;
         sysroot_flag += " -isystem" + escape_path(pp.glibcInclude);
         if (!pp.linuxInclude.empty())
             sysroot_flag += " -isystem" + escape_path(pp.linuxInclude);
         f.sysroot = sysroot_flag;
-    } else if (!plan.toolchain.sysroot.empty()) {
         sysroot_flag = " --sysroot=" + escape_path(plan.toolchain.sysroot);
         f.sysroot = sysroot_flag;
     }

src/toolchain/stdmod.cppm

@@ -129,13 +129,21 @@ std::expected<StdModule, StdModError> ensure_built(
         } else if (!tc.sysroot.empty()) {
             sysroot_flag = std::format(" --sysroot='{}'", tc.sysroot.string());
         }
+    } else if (!tc.sysroot.empty()) {
+        // GCC: use --sysroot (required for include-fixed headers).
+        // Supplement with -isystem for linux kernel headers from payload
+        // if the probed sysroot is missing them.
+        sysroot_flag = std::format(" --sysroot='{}'", tc.sysroot.string());
+        if (tc.payloadPaths && !tc.payloadPaths->linuxInclude.empty()) {
+            auto sysrootLinux = tc.sysroot / "usr" / "include" / "linux" / "limits.h";
+            if (!std::filesystem::exists(sysrootLinux))
+                sysroot_flag += std::format(" -isystem'{}'", tc.payloadPaths->linuxInclude.string());
+        }
     } else if (tc.payloadPaths) {
-        // GCC: use payload -isystem paths instead of --sysroot.
+        // No sysroot: use payload -isystem paths.
         sysroot_flag += std::format(" -isystem'{}'", tc.payloadPaths->glibcInclude.string());
         if (!tc.payloadPaths->linuxInclude.empty())
             sysroot_flag += std::format(" -isystem'{}'", tc.payloadPaths->linuxInclude.string());
-    } else if (!tc.sysroot.empty()) {
-        sysroot_flag = std::format(" --sysroot='{}'", tc.sysroot.string());
     }
 
     bool std_cached = std::filesystem::exists(sm.bmiPath) && std::filesystem::exists(sm.objectPath);