Makefile.nek compiles okay but fails at link time

Makefile.nek.in

@@ -2,15 +2,19 @@ srcdir   = @srcdir@
 VPATH    = @srcdir@/Nek5000/core:@srcdir@/Nek5000/core/cmt:@srcdir@/Nek5000/core/3rd_party:@srcdir@/Nek5000/jl
 
 
-# == Compilers and flags ======================================================
+# == Compilers and flags =======================================================
 CC        = @CC@
 CFLAGS    = @CFLAGS@
-CPPFLAGS  = @CPPFLAGS@ @DEFS@
+CPPFLAGS  = @CPPFLAGS@ @DEFS@ \
+						-I@builddir@ -I@srcdir@/Nek5000/core -I@srcdir@/Nek5000/core/cmt \
+						-I@srcdir@/Nek5000/core/3rd_party -I@srcdir@/Nek5000/jl
 LDFLAGS   = @LDFLAGS@
 LIBS      = @LIBS@
 
 F77       = @F77@
-FFLAGS    = @FFLAGS@ @FCFLAGS_f@ $(subst -D, @FC_DEFINE@, @DEFS@)
+FFLAGS    = @FFLAGS@ @FCFLAGS_f@ $(subst -D, @FC_DEFINE@, @DEFS@) \
+						-I@builddir@ -I@srcdir@/Nek5000/core -I@srcdir@/Nek5000/core/cmt \
+						-I@srcdir@/Nek5000/core/3rd_party -I@srcdir@/Nek5000/jl
 FLIBS     = @FLIBS@
 
 CASENAME    = @CASENAME@
@@ -18,7 +22,7 @@ nek_debug_flags = @nek_debug_flags@
 nek_opt_flags   = @nek_opt_flags@
 nek_real8_flags = @nek_real8_flags@
 
-# == FORTRAN objects ==========================================================
+# == FORTRAN objects ===========================================================
 nek_core_f_obj = drive.o drive1.o drive2.o \
 plan4.o bdry.o coef.o conduct.o connect1.o connect2.o \
 dssum.o edgec.o eigsolv.o gauss.o genxyz.o navier1.o makeq.o \
@@ -45,7 +49,7 @@ nek_neknek_obj = @nek_neknek_obj@  # singlmesh.o | multimesh.o
 f_obj = $(nek_core_f_obj) $(nek_math_obj) $(nek_blas_obj) $(nek_cmt_obj) \
 				$(nek_lapack_obj) $(nek_mpi_obj) $(nek_mxm_obj) $(nek_neknek_obj)
 
-# == JL objects ===============================================================
+# == C objects =================================================================
 nek_core_c_obj = byte.o chelpers.o nek_comm.o finiparser.o iniparser.o  dictionary.o
 
 jl_prefix     = @jl_prefix@
@@ -55,7 +59,7 @@ jl_cgs_obj    = $(patsubst %, $(jl_prefix)%, @jl_cgs_obj@)
 
 c_obj = $(nek_core_c_obj) $(jl_core_obj) $(jl_interp_obj) $(jl_cgs_obj)
 
-# == Rules ====================================================================
+# == Rules =====================================================================
 # A set of rules each for:
 #   * nek_core_f_obj + nek_cmt_obj + nek_mpi_obj + nek_neknek_obj
 #   * nek_math_obj + nek_mxm_obj
@@ -76,7 +80,10 @@ $(nek_math_obj) $(nek_mxm_obj): %.o : %.f SIZE
 $(nek_blas_obj) $(nek_lapack_obj): %.o: %.f SIZE
 	$(F77) -c $(FFLAGS) -O0 $(nek_debug_flags) $< -o $@
 
-$(nek_core_c_obj) $(jl_core_obj) $(jl_interp_obj) $(jl_cgs_obj): %.o: %.c
+$(nek_core_c_obj): %.o: %.c
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(nek_opt_flags) $(nek_debug_flags) $< -o $@
+
+$(jl_core_obj) $(jl_interp_obj) $(jl_cgs_obj): $(jl_prefix)%.o: %.c
 	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(nek_opt_flags) $(nek_debug_flags) $< -o $@
 
 mpiheader: