so based on the automake feedback, the suggestion is to keep bypassing the 
issue via variables.  here's the latest patch which includes fixes from Jie.

on the svf side, there's no extra dependencies as everything in that subdir 
needs the bison header files.  on the bsdl side, there is one extra 
dependency: bsdl.c depends on the bison headers.  but i dont think it's worth 
fretting about since it only comes up when checking sources out from the tree 
and regenerating autotools the first time.
-mike

--- src/bsdl/Makefile.am        (revision 1910)
+++ src/bsdl/Makefile.am        (working copy)
@@ -53,12 +53,9 @@
 # additional dependencies
 # - *_flex files must be processed after their *_bison counterparts
 #   to ensure that *_bison.h is present
-libbsdl_flex_la-vhdl_flex.$(OBJEXT): vhdl_bison.h
-libbsdl_flex_la-bsdl_flex.$(OBJEXT): bsdl_bison.h
-bsdl_sem.$(OBJEXT): bsdl_bison.h
-
-vhdl_bison.h: vhdl_bison.c
-bsdl_bison.h: bsdl_bison.c
+$(libbsdl_la_OBJECTS) $(libbsdl_flex_la_OBJECTS): bsdl_bison.h vhdl_bison.h
+vhdl_bison.h: vhdl_bison.c ; @true
+bsdl_bison.h: bsdl_bison.c ; @true
 
 AM_LFLAGS = -i
 
--- src/svf/Makefile.am (revision 1910)
+++ src/svf/Makefile.am (working copy)
@@ -35,15 +35,17 @@
 libsvf_flex_la_SOURCES = \
        svf_flex.l
 
-libsvf_flex_la-svf_flex.$(OBJEXT) svf.$(OBJEXT): svf_bison.h
-
 AM_CFLAGS = $(WARNINGCFLAGS)
 
 libsvf_flex_la_CFLAGS = \
        $(AM_CFLAGS) \
        -Wno-error
 
-svf_bison.h: svf_bison.c
+# additional dependencies
+# - *_flex files must be processed after their *_bison counterparts
+#   to ensure that *_bison.h is present
+$(libsvf_la_OBJECTS) $(libsvf_flex_la_OBJECTS): svf_bison.h
+svf_bison.h: svf_bison.c ; @true
 
 MAINTAINERCLEANFILES = \
        svf_bison.c \

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