diff --git a/apply.sh b/apply.sh
index 56dce35..8dfe396 100755
--- a/apply.sh
+++ b/apply.sh
@@ -1,4 +1,6 @@
 #!/bin/bash
+# applies the .ips patch to base.nes, generating working.nes
+# Run with -f flag to replace existing working.nes
 
 _force=false
 flips="./flips/flips.exe"
@@ -19,7 +21,8 @@ else
   then
     if [ "$_force" = false ]
     then
-      >&2 echo "working.nes already exists. Rerun with -f flag to force overwriting working.nes"
+      >&2 echo "Error: working.nes already exists."
+      >&2 echo "Rerun with -f flag to force overwriting working.nes"
       exit 1;
     else
       echo "Replacing existing working.nes"
@@ -49,6 +52,13 @@ else
   
   chmod u+x $flips
   
+  chmod u+wr working.nes
+  
   $flips --apply patch.ips working.nes
-  exit $?
+  err=$?
+  
+  chmod a-x working.nes
+  chmod u+wr working.nes
+  
+  exit $err
 fi
diff --git a/hooks/pre-commit b/hooks/pre-commit
index cb49b3b..e61a738 100755
--- a/hooks/pre-commit
+++ b/hooks/pre-commit
@@ -7,5 +7,18 @@ cd $_rdir
 # make sure base.nes and working.nes exist:
 if [ ! -f ./base.nes ]
 then
-  echo "Base ROM (base.nes) is not found!"
+  >&2 echo "Base ROM (base.nes) is not found! Aborting commit."
+  exit 1;
 fi
+
+if [ ! -f ./base.nes ]
+then
+  >&2 echo "Modified ROM (working.nes) is not found! Aborting commit."
+  >&2 echo "(Did you ever generate working.nes with apply.sh?)"
+  exit 2;
+fi
+
+# generate patch
+./make-patch.sh
+
+exit $?
diff --git a/make-patch.sh b/make-patch.sh
new file mode 100755
index 0000000..1ad3636
--- /dev/null
+++ b/make-patch.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+# creates a patch based on the difference between base.rom and working.rom
+
+# find flips patcher:
+flips="./flips/flips.exe"
+
+if [ "$op" = "Linux" ]
+then
+  flips="./flips/flips-linux"
+fi
+
+if [ ! -f $flips ]
+then
+    >&2 echo "flips not found; do you have the flips/ folder?"
+    exit 2;
+fi
+
+echo "Generating patch.ips..."
+
+chmod u+w patch.ips
+
+rm patch.ips
+
+$flips --create --ips base.nes working.nes patch.ips
+err=$?
+
+chmod u+r patch.ips
+chmod a-wx patch.ips
+
+exit $?
diff --git a/setup.sh b/setup.sh
index 7723636..5528712 100755
--- a/setup.sh
+++ b/setup.sh
@@ -23,6 +23,9 @@ else
   then
     echo "Warning: working.nes but no base.nes file; you will not be able to generate patches."
     echo "(Perhaps you should delete working.nes and copy in a new base.nes?)"
+  else
+    echo "No changes made to base.nes or working.nes"
+    echo "(If you intended to apply the patch now, then run ./apply.sh)"
   fi
 fi