fix and simplify

- avoid adding "include Makefile_taf.dep" multiple times at bottom of Makefile
  by doing this as part of "make depend"
- simplify `f90mkdepend_taf` (remove "-clean" option) and pass name of output file
  as first argument.
- add 1 line to "Clean" target to remove "include Makefile_taf.dep" from bottom
  of Makefile and, if sucessful, remove file "Makefile_taf.dep".

tools/f90mkdepend_taf

@@ -1,59 +1,27 @@
 #!/bin/bash
 #
 # Generate make file dependency entries for TAF generated AD files
-# passed as arguments
-#
-
-# process option arguments
-CLEAN=
-adfiles=
-key_prev=
-for key in "$@"; do
-    if [[ -n "$key_prev" ]]; then
-        eval "$key_prev=\$key"
-        key_prev=
-        continue
-    fi
+# passed as arguments after output dependency file
 
-    case $key in
-    -clean | --clean)
-        CLEAN=true
-        ;;
-    -taf | --taf)
-        key_prev="adfiles"
-        ;;
-    -*)
-        echo "f90mkdepend_taf wrong key: $key"
-        exit 1
-        ;;
-    *)
-        # Append non-option arguments to adfiles
-        adfiles="${adfiles:+$adfiles }$key"
-        ;;
-    esac
-done
+if [ $# -eq 0 ]; then
+  echo "Usage: `basename $0` output_file list_of_TAF_generated_files"
+  exit 1
+else
+  dep_file=$1 ; shift
+fi
 
 # don't complain if *.F90 doesn't match any files
 shopt -s nullglob
 
 # init files
+#log_file="`basename $0`.log"
 log_file="f90mkdepend_taf.log"
-dep_file="Makefile_taf.dep"
 
 cat /dev/null > $log_file
 cat /dev/null > $dep_file
 
-# OPTION to clean Makefile of $dep_file
-MAKEFILE=Makefile
-if test -n "$CLEAN"; then
-    if [[ $(tail -n 1 $MAKEFILE) == "include $dep_file" ]]; then
-        head -n -1 $MAKEFILE > tmp && mv tmp $MAKEFILE
-    fi
-    rm -rf $dep_file $log_file
-    exit 0
-fi
-
 # append module dependencies to Makefile
+adfiles=$*
 for filename in ${adfiles}; do
   # quick check for "use" to speed up processing
   if grep -iq '^ *use ' $filename; then
@@ -79,5 +47,4 @@ for filename in ${adfiles}; do
     echo $depline >> $dep_file
   fi
 done
-
-echo "include $dep_file"
+exit 0

tools/genmake2

@@ -1425,6 +1425,7 @@ TAPENADECMD=tapenade
 OPENAD=
 AD_OPTFILE=
 CAT_SRC_FOR_TAF=1
+DEP_TAF_FILE='Makefile_taf.dep'
 TAF=
 AD_TAF_FLAGS=
 FTL_TAF_FLAGS=
@@ -3361,6 +3362,12 @@ depend:
 	\$(MAKEDEPEND) -f \$(MAKEFILE) -a -o .$FS90 \$(DEFINES) \$(INCLUDES) \$(CPPINCLUDES) \$(F90_SRC_FILES)
 	\$(TOOLSDIR)/f90mkdepend -fs $FS -fs90 $FS90 >> \$(MAKEFILE)
 	-rm -f makedepend.out
+EOF
+if test $CAT_SRC_FOR_TAF = 0 ; then
+  echo "	-touch $DEP_TAF_FILE" >> $MAKEFILE
+  echo "	-echo 'include $DEP_TAF_FILE' >> \$(MAKEFILE)" >> $MAKEFILE
+fi
+cat >>$MAKEFILE <<EOF
 
 lib: libmitgcmuv.a
 
@@ -3387,9 +3394,15 @@ Clean:
 	@\$(MAKE) -f \$(MAKEFILE) cleanlinks
 	-rm -rf *.flowdir
 	-rm -f \$(SPECIAL_FILES) f90mkdepend.log $MAKEFILE.old
-	-rm -f taf_ad.f90
 	-rm -f taf_command taf_output taf_ad.log taf_ad_flow.log taf_ftl.log
-	-\$(TOOLSDIR)/f90mkdepend_taf -clean
+EOF
+if test $CAT_SRC_FOR_TAF = 0 ; then
+cat >>$MAKEFILE <<EOF
+	-sed "/^include $DEP_TAF_FILE/d" \$(MAKEFILE) > tmp_Mkfile && mv -f tmp_Mkfile \$(MAKEFILE) && rm -f $DEP_TAF_FILE
+	-rm -f taf_ad.f90 taf_tl.f90 f90mkdepend_taf.log
+EOF
+fi
+cat >>$MAKEFILE <<EOF
 
 # remove also the executable, files that "genmake2" generates (except Makefile)
 #         and output from a run (plus log files from testreport)
@@ -3631,7 +3644,7 @@ else
 cat >>$MAKEFILE <<EOF
 # ... send multiple files to TAF ...
 adj_depend:
-	\$(TOOLSDIR)/f90mkdepend_taf -taf \$(AD_F90FILES:.$FS90=_ad.$FS90) \$(AD_FILES:.$FS=_ad.$FS) >> \$(MAKEFILE)
+	\$(TOOLSDIR)/f90mkdepend_taf $DEP_TAF_FILE \$(AD_F90FILES:.$FS90=_ad.$FS90) \$(AD_FILES:.$FS=_ad.$FS)
 
 ad_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_F90FILES) \$(AD_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "Adjoint version" -bAD_CONFIG_H -DALLOW_ADJOINT_RUN -UALLOW_TANGENTLINEAR_RUN > ad_config.template
@@ -3739,7 +3752,7 @@ else
 cat >>$MAKEFILE <<EOF
 # ... send multiple files to TAF ...
 ftl_depend:
-	\$(TOOLSDIR)/f90mkdepend_taf -taf \$(AD_F90FILES:.$FS90=_tl.$FS90) \$(AD_FILES:.$FS=_tl.$FS) >> \$(MAKEFILE)
+	\$(TOOLSDIR)/f90mkdepend_taf $DEP_TAF_FILE \$(AD_F90FILES:.$FS90=_tl.$FS90) \$(AD_FILES:.$FS=_tl.$FS)
 
 ftl_taf_output.$FS: \$(AD_FLOW_FILES) \$(AD_F90FILES) \$(AD_FILES)
 	@$BASH\$(TOOLSDIR)/convert_cpp_cmd2defines "TangLin version" -bAD_CONFIG_H -UALLOW_ADJOINT_RUN -DALLOW_TANGENTLINEAR_RUN > ad_config.template