--- emcc.py
+++ emcc.py
@@ -206,6 +206,9 @@ class EmccOptions(object):
     # Defaults to using the native EOL on each platform (\r\n on Windows, \n on
     # Linux & MacOS)
     self.output_eol = os.linesep
+    # Whether we will expand the full path of any input files to remove any
+    # symlinks.
+    self.expand_symlinks = True


 def use_source_map(options):
@@ -859,7 +862,9 @@ There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR P
                     '-current_version', '-I', '-L', '-include-pch'):
           continue # ignore this gcc-style argument

-      if os.path.islink(arg) and get_file_suffix(os.path.realpath(arg)) in SOURCE_ENDINGS + BITCODE_ENDINGS + DYNAMICLIB_ENDINGS + ASSEMBLY_ENDINGS + HEADER_ENDINGS:
+      if (options.expand_symlinks
+          and os.path.islink(arg)
+          and get_file_suffix(os.path.realpath(arg)) in SOURCE_ENDINGS + BITCODE_ENDINGS + DYNAMICLIB_ENDINGS + ASSEMBLY_ENDINGS + HEADER_ENDINGS):
         arg = os.path.realpath(arg)

       if not arg.startswith('-'):
@@ -2516,6 +2521,8 @@ def parse_args(newargs):
       settings_changes.append('SIMD=1')
     elif newargs[i] == '-mno-simd128':
       settings_changes.append('SIMD=0')
+    elif newargs[i] == '-no-canonical-prefixes':
+      options.expand_symlinks = False

   if should_exit:
     sys.exit(0)
--- tools/system_libs.py
+++ tools/system_libs.py
@@ -89,10 +89,20 @@ def calculate(temp_files, in_temp, stdout_, stderr_, forced=[]):
       if os.name != 'nt' and '\r\n' in content:
         raise Exception('Windows newlines \\r\\n detected in symbols file "' + path + '"! This could happen for example when copying Emscripten checkout from Windows to Linux or macOS. Please use Unix line endings on checkouts of Emscripten on Linux and macOS!')

       return shared.Building.parse_symbols(content).defs

-  default_opts = ['-Werror']
+  default_opts = ['-Werror',
+                  '-isystem',
+                  shared.path_from_root('system', 'include'),
+                  '-isystem',
+                  shared.path_from_root('system', 'include', 'libcxx'),
+                  '-isystem',
+                  shared.path_from_root('system', 'lib', 'libc', 'musl', 'arch', 'emscripten'),
+                  '-isystem',
+                  shared.path_from_root('system', 'include', 'compat'),
+                  '-isystem',
+                  shared.path_from_root('system', 'include', 'libc')]

   # XXX We also need to add libc symbols that use malloc, for example strdup. It's very rare to use just them and not
   #     a normal malloc symbol (like free, after calling strdup), so we haven't hit this yet, but it is possible.
   libc_symbols = read_symbols(shared.path_from_root('system', 'lib', 'libc.symbols'))
@@ -426,5 +436,5 @@ def calculate(temp_files, in_temp, stdout_, stderr_, forced=[]):
   def create_al(libname): # libname is ignored, this is just one .o file
     o = in_temp('al.o')
-    check_call([shared.PYTHON, shared.EMCC, shared.path_from_root('system', 'lib', 'al.c'), '-o', o, '-Os'] + get_cflags())
+    check_call([shared.PYTHON, shared.EMCC, shared.path_from_root('system', 'lib', 'al.c'), '-o', o, '-Os'] + get_cflags() + default_opts)
     return o

@@ -447,5 +455,5 @@ def create_compiler_rt(libname):
     for src in files:
       o = in_temp(os.path.basename(src) + '.o')
-      commands.append([shared.PYTHON, shared.EMCC, shared.path_from_root('system', 'lib', src), '-O2', '-o', o] + get_cflags())
+      commands.append([shared.PYTHON, shared.EMCC, shared.path_from_root('system', 'lib', src), '-O2', '-o', o] + get_cflags() + default_opts)
       o_s.append(o)
     run_commands(commands)
@@ -500,5 +506,5 @@ def calculate(temp_files, in_temp, stdout_, stderr_, forced=[]):
   def create_malloc(out_name):
     o = in_temp(out_name)
-    cflags = ['-O2', '-fno-builtin']
+    cflags = default_opts + ['-O2', '-fno-builtin']
     if shared.Settings.USE_PTHREADS:
       cflags += ['-s', 'USE_PTHREADS=1']
--- tools/gen_struct_info.py
+++ tools/gen_struct_info.py
@@ -401,4 +401,12 @@ def inspect_code(headers, cpp_opts, structs, defines):
   # Compile the program.
   show('Compiling generated code...')
+  cpp_opts += ['-isystem',
+               shared.path_from_root('system', 'include'),
+               '-isystem',
+               shared.path_from_root('system', 'include', 'libcxx'),
+               '-isystem',
+               shared.path_from_root('system', 'lib', 'libc', 'musl', 'arch', 'emscripten'),
+               '-isystem',
+               shared.path_from_root('system', 'include', 'libc')]
   # -Oz optimizes enough to avoid warnings on code size/num locals
   cmd = [shared.PYTHON, shared.EMCC] + cpp_opts + ['-o', js_file[1], src_file[1], '-s', 'BOOTSTRAPPING_STRUCT_INFO=1', '-s', 'WARN_ON_UNDEFINED_SYMBOLS=0', '-O0', '--js-opts', '0', '--memory-init-file', '0', '-s', 'SINGLE_FILE=1', '-Wno-format']