Finer choice of files to update in regtest script

removes spurious error messages

namd/tests/library/run_tests.sh

@@ -100,7 +100,7 @@ cleanup_files() {
     fi
     for f in ${script%.namd}.*diff; do if [ ! -s $f ]; then rm -f $f; fi; done # remove empty diffs only
     rm -f ${script%.namd}.*{BAK,old,backup}
-    for f in ${script%.namd}.*{state,state.stripped,out,traj,coor,vel,xsc,dcd,pmf,hills,grad,force,count,histogram?.dat,hist.dat,corrfunc.dat,histogram?.dx,count.dx,pmf.dx,output.dat}
+    for f in ${script%.namd}.*{state,state.stripped,out,traj,coor,vel,xsc,dcd,pmf,hills,grad,force,count,histogram?.dat,hist.dat,corrfunc.dat,histogram?.dx,count.dx,pmf.dx,output.dat,ti}
     do
       if [ ! -f "$f.diff" ]; then rm -f $f; fi # keep files that have a non-empty diff
     done
@@ -221,8 +221,11 @@ for dir in ${DIRLIST} ; do
       fi
 
       # Update any additional files with current versions
-      for file in AutoDiff/*; do
-        cp -uf `basename ${file}` AutoDiff/
+      for file in AutoDiff/${basename}*; do
+        source=`basename ${file}`
+        if [ -f ${source} ] ; then
+          cp -uf ${source} AutoDiff/
+        fi
       done
     fi