diff --git a/src/Makefile b/src/Makefile
index 33780d0..0b86b46 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1279,10 +1279,6 @@
 #     -D"foo()=" is not supported by all compilers so do not use it
 NO_ATTR=
 #
-#     maybe the "/usr/bin/cc -E" has to be adjusted for some systems
-# This is for cproto 3.5 patchlevel 3:
-# PROTO_FLAGS = -f4 -m__ARGS -d -E"$(CPP)" $(NO_ATTR)
-#
 # Use this for cproto 3 patchlevel 6 or below (use "cproto -V" to check):
 # PROTO_FLAGS = -f4 -m__ARGS -d -E"$(CPP)" $(NO_ATTR)
 #
@@ -1300,10 +1296,9 @@
 .SUFFIXES: .c .o .pro
 
 PRE_DEFS = -Iproto $(DEFS) $(GUI_DEFS) $(GUI_IPATH) $(CPPFLAGS) $(EXTRA_IPATHS)
-POST_DEFS = $(X_CFLAGS) $(MZSCHEME_CFLAGS) $(PERL_CFLAGS) $(PYTHON_CFLAGS) $(TCL_CFLAGS) $(RUBY_CFLAGS) $(EXTRA_DEFS)
-NOPROTO_DEFS = $(PYTHON_NOPROTO)
+POST_DEFS = $(X_CFLAGS) $(MZSCHEME_CFLAGS) $(PERL_CFLAGS) $(ECL_CFLAGS) $(PYTHON_CFLAGS) $(TCL_CFLAGS) $(RUBY_CFLAGS) $(EXTRA_DEFS)
 
-ALL_CFLAGS = $(PRE_DEFS) $(CFLAGS) $(PROFILE_CFLAGS) $(POST_DEFS) $(NOPROTO_DEFS)
+ALL_CFLAGS = $(PRE_DEFS) $(CFLAGS) $(PROFILE_CFLAGS) $(POST_DEFS)
 
 # Exclude $CFLAGS for osdef.sh, for Mac 10.4 some flags don't work together
 # with "-E".
@@ -1315,11 +1310,6 @@
 
 DEPEND_CFLAGS = -DPROTO -DDEPEND -DFEAT_GUI $(LINT_CFLAGS)
 
-# If you have problems with flags that cproto doesn't support, and you are
-# using GNU make, you can try using the other line to filter out arguments.
-#PFLAGS = $(PROTO_FLAGS) -DPROTO $(filter -D% -I%, $(LINT_CFLAGS))
-PFLAGS = $(PROTO_FLAGS) -DPROTO $(LINT_CFLAGS)
-
 ALL_LIB_DIRS = $(GUI_LIBS_DIR) $(X_LIBS_DIR)
 ALL_LIBS = $(GUI_LIBS1) $(GUI_X_LIBS) $(GUI_LIBS2) $(X_PRE_LIBS) $(X_LIBS) $(X_EXTRA_LIBS) $(LIBS) $(EXTRA_LIBS) $(MZSCHEME_LIBS) $(PERL_LIBS) $(PYTHON_LIBS) $(TCL_LIBS) $(RUBY_LIBS) $(PROFILE_LIBS)
 
@@ -1680,46 +1670,53 @@
 
 proto: $(PRO_AUTO) $(PRO_MANUAL)
 
+# Filter out arguments that cproto doesn't support.
+# Don't pass "-pthread" to cproto, it sees it as a list of individual flags.
+# The -E"gcc -E" argument must be separate to avoid problems with shell
+# quoting.
+CPROTO = cproto $(PROTO_FLAGS) -DPROTO \
+	 `echo '$(LINT_CFLAGS)' | sed -e 's/-pthread//g'` 
+
 ### Would be nice if this would work for "normal" make.
 ### Currently it only works for (Free)BSD make.
 #$(PRO_AUTO): $$(*F).c
-#	cproto $(PFLAGS) -DFEAT_GUI $(*F).c > $@
+#	$(CPROTO) -DFEAT_GUI $(*F).c > $@
 
 # Always define FEAT_GUI.  This may generate a few warnings if it's also
 # defined in auto/config.h, you can ignore that.
 .c.pro:
-	cproto $(PFLAGS) -DFEAT_GUI $< > proto/$@
+	$(CPROTO) -DFEAT_GUI $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_amiga.pro: os_amiga.c
-	cproto $(PFLAGS) -DAMIGA -UHAVE_CONFIG_H -DBPTR=char* $< > proto/$@
+	$(CPROTO) -DAMIGA -UHAVE_CONFIG_H -DBPTR=char* $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_msdos.pro: os_msdos.c
-	cproto $(PFLAGS) -DMSDOS -UHAVE_CONFIG_H $< > proto/$@
+	$(CPROTO) -DMSDOS -UHAVE_CONFIG_H $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_win16.pro: os_win16.c
-	cproto $(PFLAGS) -DWIN16 -UHAVE_CONFIG_H $< > proto/$@
+	$(CPROTO) -DWIN16 -UHAVE_CONFIG_H $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_win32.pro: os_win32.c
-	cproto $(PFLAGS) -DWIN32 -UHAVE_CONFIG_H $< > proto/$@
+	$(CPROTO) -DWIN32 -UHAVE_CONFIG_H $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_mswin.pro: os_mswin.c
-	cproto $(PFLAGS) -DWIN16 -DWIN32 -UHAVE_CONFIG_H $< > proto/$@
+	$(CPROTO) -DWIN16 -DWIN32 -UHAVE_CONFIG_H $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_beos.pro: os_beos.c
-	cproto $(PFLAGS) -D__BEOS__ -UHAVE_CONFIG_H $< > proto/$@
+	$(CPROTO) -D__BEOS__ -UHAVE_CONFIG_H $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 
 os_vms.pro: os_vms.c
 # must use os_vms_conf.h for auto/config.h
 	mv auto/config.h auto/config.h.save
 	cp os_vms_conf.h auto/config.h
-	cproto $(PFLAGS) -DVMS -UFEAT_GUI_ATHENA -UFEAT_GUI_NEXTAW -UFEAT_GUI_MOTIF -UFEAT_GUI_GTK $< > proto/$@
+	$(CPROTO) -DVMS -UFEAT_GUI_ATHENA -UFEAT_GUI_NEXTAW -UFEAT_GUI_MOTIF -UFEAT_GUI_GTK $< > proto/$@
 	echo "/* vim: set ft=c : */" >> proto/$@
 	rm auto/config.h
 	mv auto/config.h.save auto/config.h
@@ -1727,7 +1724,7 @@
 # if_perl.pro is special: Use the generated if_perl.c for input and remove
 # prototypes for local functions.
 if_perl.pro: auto/if_perl.c
-	cproto $(PFLAGS) -DFEAT_GUI auto/if_perl.c | sed "/_VI/d" > proto/$@
+	$(CPROTO) -DFEAT_GUI auto/if_perl.c | sed "/_VI/d" > proto/$@
 
 
 notags:
diff --git a/src/auto/configure b/src/auto/configure
index 5e0e57a..20f723b 100755
--- a/src/auto/configure
+++ b/src/auto/configure
@@ -641,7 +641,6 @@
 vi_cv_path_tcl
 PYTHON_OBJ
 PYTHON_SRC
-PYTHON_NOPROTO
 PYTHON_CFLAGS
 PYTHON_GETPATH_CFLAGS
 PYTHON_LIBS
@@ -5112,7 +5111,6 @@
 	else
 	  PYTHON_CFLAGS="-I${vi_cv_path_python_pfx}/include/python${vi_cv_var_python_version} -I${vi_cv_path_python_epfx}/include/python${vi_cv_var_python_version}"
 	fi
-	PYTHON_NOPROTO=
 	PYTHON_SRC="if_python.c"
 		if test "x$MACOSX" = "xyes"; then
 	  PYTHON_OBJ="objects/if_python.o"
@@ -5124,7 +5122,7 @@
 	fi
 	PYTHON_GETPATH_CFLAGS="-DPYTHONPATH='\"${vi_cv_path_pythonpath}\"' -DPREFIX='\"${vi_cv_path_python_pfx}\"' -DEXEC_PREFIX='\"${vi_cv_path_python_epfx}\"'"
 
-										{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if -pthread should be used" >&5
+								{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if -pthread should be used" >&5
 $as_echo_n "checking if -pthread should be used... " >&6; }
 	threadsafe_flag=
 	thread_lib=
@@ -5153,7 +5151,7 @@
 _ACEOF
 if ac_fn_c_try_link "$LINENO"; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }; PYTHON_NOPROTO="$threadsafe_flag"
+$as_echo "yes" >&6; }; PYTHON_CFLAGS="$PYTHON_CFLAGS $threadsafe_flag"
 else
   { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }; LIBS=$libs_save_old
@@ -5171,7 +5169,7 @@
 $as_echo_n "checking if compile and link flags for Python are sane... " >&6; }
 	cflags_save=$CFLAGS
 	libs_save=$LIBS
-	CFLAGS="$CFLAGS $PYTHON_CFLAGS $PYTHON_NOPROTO"
+	CFLAGS="$CFLAGS $PYTHON_CFLAGS"
 	LIBS="$LIBS $PYTHON_LIBS"
 	cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -5204,7 +5202,6 @@
 	  PYTHON_OBJ=
 	  PYTHON_LIBS=
 	  PYTHON_CFLAGS=
-	  PYTHON_NOPROTO=
 	fi
 
       fi
@@ -5221,7 +5218,6 @@
 
 
 
-
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking --enable-tclinterp argument" >&5
 $as_echo_n "checking --enable-tclinterp argument... " >&6; }
 # Check whether --enable-tclinterp was given.
diff --git a/src/config.mk.in b/src/config.mk.in
index a298fae..2586558 100644
--- a/src/config.mk.in
+++ b/src/config.mk.in
@@ -56,7 +56,6 @@
 PYTHON_SRC	= @PYTHON_SRC@
 PYTHON_OBJ	= @PYTHON_OBJ@
 PYTHON_CFLAGS	= @PYTHON_CFLAGS@
-PYTHON_NOPROTO	= @PYTHON_NOPROTO@
 PYTHON_LIBS	= @PYTHON_LIBS@
 PYTHON_CONFDIR	= @PYTHON_CONFDIR@
 PYTHON_GETPATH_CFLAGS = @PYTHON_GETPATH_CFLAGS@
diff --git a/src/configure.in b/src/configure.in
index a18c683..567c7a2 100644
--- a/src/configure.in
+++ b/src/configure.in
@@ -764,7 +764,6 @@
 	else
 	  PYTHON_CFLAGS="-I${vi_cv_path_python_pfx}/include/python${vi_cv_var_python_version} -I${vi_cv_path_python_epfx}/include/python${vi_cv_var_python_version}"
 	fi
-	PYTHON_NOPROTO=
 	PYTHON_SRC="if_python.c"
 	dnl For Mac OSX 10.2 config.o is included in the Python library.
 	if test "x$MACOSX" = "xyes"; then
@@ -784,8 +783,6 @@
 	dnl Otherwise, when using GCC, try adding -pthread to $CFLAGS.  GCC
 	dnl will then define target-specific defines, e.g., -D_REENTRANT.
 	dnl Don't do this for Mac OSX, -pthread will generate a warning.
-	dnl Need to put -pthread in PYTHON_NOPROTO, because it cannot be used
-	dnl for cproto.
 	AC_MSG_CHECKING([if -pthread should be used])
 	threadsafe_flag=
 	thread_lib=
@@ -803,7 +800,7 @@
 	  CFLAGS="$CFLAGS $threadsafe_flag"
 	  LIBS="$LIBS $thread_lib"
 	  AC_TRY_LINK(,[ ],
-	     AC_MSG_RESULT(yes); PYTHON_NOPROTO="$threadsafe_flag",
+	     AC_MSG_RESULT(yes); PYTHON_CFLAGS="$PYTHON_CFLAGS $threadsafe_flag",
 	     AC_MSG_RESULT(no); LIBS=$libs_save_old
 	     )
 	  CFLAGS=$cflags_save
@@ -816,7 +813,7 @@
 	AC_MSG_CHECKING([if compile and link flags for Python are sane])
 	cflags_save=$CFLAGS
 	libs_save=$LIBS
-	CFLAGS="$CFLAGS $PYTHON_CFLAGS $PYTHON_NOPROTO"
+	CFLAGS="$CFLAGS $PYTHON_CFLAGS"
 	LIBS="$LIBS $PYTHON_LIBS"
 	AC_TRY_LINK(,[ ],
 	       AC_MSG_RESULT(yes); python_ok=yes,
@@ -831,7 +828,6 @@
 	  PYTHON_OBJ=
 	  PYTHON_LIBS=
 	  PYTHON_CFLAGS=
-	  PYTHON_NOPROTO=
 	fi
 
       fi
@@ -844,7 +840,6 @@
 AC_SUBST(PYTHON_LIBS)
 AC_SUBST(PYTHON_GETPATH_CFLAGS)
 AC_SUBST(PYTHON_CFLAGS)
-AC_SUBST(PYTHON_NOPROTO)
 AC_SUBST(PYTHON_SRC)
 AC_SUBST(PYTHON_OBJ)