Use configure to produce a gfc script with the correct path to gf3. NOTE: you need to re-run autoconf after pulling this patch.

src/gfc.in

@@ -0,0 +1,25 @@
+#!/bin/sh
+
+prefix="@prefix@"
+
+case "@host@" in
+      *-cygwin)
+          prefix=`cygpath -w "$prefix"`;;
+esac
+
+exec_prefix="@exec_prefix@"
+GF_BIN_DIR="@bindir@"
+GF_DATA_DIR="@datadir@/GF-@PACKAGE_VERSION@"
+
+GFBIN="$GF_BIN_DIR/gf3"
+
+if [ ! -x "${GFBIN}" ]; then
+   GFBIN=`which gf3`
+fi
+
+if [ ! -x "${GFBIN}" ]; then
+    echo "gf3 not found."
+    exit 1
+fi
+
+exec $GFBIN --batch "$@"