Fix cache repopulation within emconfigure (#16986)

When `emcc` is called within `emconfigure` and also needs to build a
cache from scratch, it incorrectly retains the
`EMMAKEN_JUST_CONFIGURE` variable for the cache build, causing errors.

Author: duxovni

tests/test_other.py

@@ -5526,6 +5526,11 @@ def check(what, args, fail=True, expect=''):
 ''')
     check(EMCONFIGURE, [PYTHON, 'test.py'], expect=shared.LLVM_NM, fail=False)
 
+    create_file('test.c', 'int main() { return 0; }')
+    os.mkdir('test_cache')
+    with env_modify({'EM_CACHE': os.path.abspath('test_cache')}):
+      check(EMCONFIGURE, [EMCC, 'test.c'], fail=False)
+
   def test_emmake_python(self):
     # simulates a configure/make script that looks for things like CC, AR, etc., and which we should
     # not confuse by setting those vars to something containing `python X` as the script checks for

tools/system_libs.py

@@ -62,7 +62,8 @@ def clean_env():
   for opt in ['CFLAGS', 'CXXFLAGS', 'LDFLAGS',
               'EMCC_CFLAGS',
               'EMCC_FORCE_STDLIBS',
-              'EMCC_ONLY_FORCED_STDLIBS']:
+              'EMCC_ONLY_FORCED_STDLIBS',
+              'EMMAKEN_JUST_CONFIGURE']:
     if opt in safe_env:
       del safe_env[opt]
   return safe_env