diff --git a/Actions.hs b/Actions.hs
--- a/Actions.hs
+++ b/Actions.hs
@@ -30,7 +30,8 @@
       Exec x -> action_exec x ri resultlist
 
 formatBin :: RunInfo -> Integer -> String
-formatBin ri bin = printf (binFmt ri) bin
+formatBin ri bin = 
+   printf (binFmt ri) bin
 
 action_print :: RunInfo -> [(Integer, [FilePath])] -> IO ()
 action_print ri =
@@ -63,8 +64,12 @@
     where makeLink (bin, fpl) = 
               mapM_ (makeLink' (formatBin ri bin)) fpl
           makeLink' bin fp =
-              do createDirectoryIfMissing False bin
-                 func fp (bin ++ "/" ++ takeFileName fp)
+              if deepLinks ri
+                 then do let dirname = bin ++ "/" ++ takeDirectory fp
+                         createDirectoryIfMissing True dirname
+                         func fp (dirname ++ "/" ++ takeFileName fp)
+                 else do createDirectoryIfMissing False bin
+                         func fp (bin ++ "/" ++ takeFileName fp)
 
 action_exec :: String -> RunInfo -> [(Integer, [FilePath])] -> IO ()
 action_exec cmd ri inp =
diff --git a/Types.hs b/Types.hs
--- a/Types.hs
+++ b/Types.hs
@@ -16,6 +16,8 @@
     RunInfo {binSize :: Integer,
              firstBinSize :: Integer,
              preserveOrder :: Bool,
+             sortFiles :: Bool,
+             deepLinks :: Bool,
              readNull :: Bool,
              binFmt :: String,
              action :: Action}
diff --git a/datapacker.cabal b/datapacker.cabal
--- a/datapacker.cabal
+++ b/datapacker.cabal
@@ -1,5 +1,5 @@
 Name: datapacker
-Version: 1.0.0.1
+Version: 1.0.1
 License: GPL
 Maintainer: John Goerzen <jgoerzen@complete.org>
 Author: John Goerzen
diff --git a/datapacker.hs b/datapacker.hs
--- a/datapacker.hs
+++ b/datapacker.hs
@@ -62,12 +62,14 @@
                   \Tip: this can include a directory.\n\
                   \default: %03d",
            Option "d" ["debug"] (NoArg ("d", "")) "Enable debugging",
+           Option "D" ["deep-links"] (NoArg ("D", "")) "Enable deep bin directories",
            Option "p" ["preserve-order"] (NoArg ("p", ""))
                   "Don't reorder files for maximum packing",
            Option "s" ["size"] (ReqArg (stdRequired "s") "SIZE")
                   "Size of each output bin",
            Option "S" ["size-first"] (ReqArg (stdRequired "S") "SIZE")
                   "Override size of first output bin",
+           Option "" ["sort"] (NoArg ("sort", "")) "Sort input; useless without -p",
            Option "" ["help"] (NoArg ("help", "")) "Display this help"]
 
 worker :: [(String, String)] -> [FilePath] -> IO ()
@@ -89,7 +91,9 @@
                         then readFileList (readNull runinfo)
                         else return files
 
-       results <- scan runinfo files_scan
+       let listToProc = if sortFiles runinfo then sort files_scan else files_scan
+
+       results <- scan runinfo listToProc
        let numberedResults = zip [1..] (map (map snd) results)
        runAction runinfo numberedResults
 
@@ -118,6 +122,12 @@
        let b = case lookup "b" args of
                  Nothing -> "%03d"
                  Just x -> x
+       let deeplinks = case lookup "D" args of
+                        Nothing -> False
+                        Just _ -> True
+       let dosort = case lookup "sort" args of
+                      Nothing -> False
+                      Just _ -> True
        a <- case lookup "a" args of
               Nothing -> return Print
               Just "print" -> return Print
@@ -131,7 +141,7 @@
                      else fail $ "Unknown action: " ++ show x
        return $ RunInfo {binSize = size, firstBinSize = first,
                          preserveOrder = po, readNull = n, binFmt = b,
-                         action = a}
+                         action = a, deepLinks = deeplinks, sortFiles = dosort}
 
 usageerror :: String -> IO t
 usageerror errormsg =
diff --git a/datapacker.sgml b/datapacker.sgml
--- a/datapacker.sgml
+++ b/datapacker.sgml
@@ -206,6 +206,9 @@
                     with the same filename in different paths.
                     &datapacker; will exit on either of these situations.
                   </para>
+                  <para>
+                    See also <option>--deep-links</option>.
+                  </para>
                 </listitem>
               </varlistentry>
 
@@ -220,6 +223,8 @@
                   single filename occur in multiple input directories
                   with this option.
                   </para>
+                  <para>
+                    See also <option>--deep-links</option>.
                 </listitem>
               </varlistentry>
             </variablelist>
@@ -264,6 +269,22 @@
         </varlistentry>
 
         <varlistentry>
+          <term>-D</term>
+          <term>--deep-links</term>
+          <listitem>
+            <para>
+              When used with the symlink or hardlink action, instead
+              of making all links in a single flat directory under the
+              bin, mimic the source directory structure under the
+              bin.  Makes most sense when used with
+              <option>-p</option>, but could also be useful without it
+              if there are files with the same name in different
+              source directories.
+            </para>
+          </listitem>
+        </varlistentry>
+
+        <varlistentry>
           <term>--help</term>
           <listitem>
             <para>
@@ -361,6 +382,20 @@
             </para>
           </listitem>
         </varlistentry>
+
+        <varlistentry>
+          <term>--sort</term>
+          <listitem>
+            <para>
+              Sorts the list of files to process before acting upon
+              them.  When combined with <option>-p</option>, causes
+              the output to be sorted.  This option has no effect save
+              increasing CPU usage when not combined with
+              <option>-p</option>.
+            </para>
+          </listitem>
+        </varlistentry>
+
       </variablelist>
       <refsect2>
         <title>File Specification</title>