diff -urN rebase-4.4.1.orig/rebase.c rebase-4.4.1/rebase.c
--- rebase-4.4.1.orig/rebase.c	2014-06-14 14:11:24.073986700 +0100
+++ rebase-4.4.1/rebase.c	2014-06-14 23:18:28.632106000 +0100
@@ -42,6 +42,7 @@
 
 BOOL save_image_info ();
 BOOL load_image_info ();
+void dedupe_image_info ();
 BOOL merge_image_info ();
 BOOL collect_image_info (const char *pathname);
 void print_image_info ();
@@ -67,6 +68,12 @@
 BOOL image_storage_flag = FALSE;
 BOOL image_oblivious_flag = FALSE;
 BOOL force_rebase_flag = FALSE;
+/* Added to support MSYS2. If you do not use database mode (-s)
+then the files are not sorted by name. Also, duplicates are
+not removed from the list as a pre-process. Instead, a linear
+search is performed over the already-processed files and if
+the file in question was already done then it is skipped. */
+BOOL obey_order_flag = FALSE;
 ULONG offset = 0;
 int args_index = 0;
 BOOL verbose = FALSE;
@@ -193,6 +200,12 @@
     }
 #endif /* __CYGWIN__ */
 
+  /* Start from here .. */
+  if (obey_order_flag)
+    {
+	  image_base = cygwin_dll_image_base + cygwin_dll_image_size;
+	}
+
   /* Collect file list, if specified. */
   if (file_list)
     {
@@ -241,6 +254,8 @@
     }
   else if (!image_storage_flag)
     {
+      dedupe_image_info ();
+
       /* Rebase. */
       ULONG64 new_image_base = image_base;
       for (i = 0; i < img_info_size; ++i)
@@ -583,32 +598,46 @@
   return img->flag.cannot_rebase;
 }
 
-int
-merge_image_info ()
+void
+dedupe_image_info ()
 {
-  int i, end;
-  img_info_t *match;
-  ULONG64 floating_image_base;
+  int i, j;
 
-  /* Sort new files from command line by name. */
-  qsort (img_info_list + img_info_rebase_start,
-	 img_info_size - img_info_rebase_start, sizeof (img_info_t),
-	 img_info_name_cmp);
+  if (!obey_order_flag)
+    {
+    /* Sort new files from command line by name. */
+    qsort (img_info_list + img_info_rebase_start,
+	   img_info_size - img_info_rebase_start, sizeof (img_info_t),
+	   img_info_name_cmp);
+	}
   /* Iterate through new files and eliminate duplicates. */
   for (i = img_info_rebase_start; i + 1 < img_info_size; ++i)
-    if ((img_info_list[i].name_size == img_info_list[i + 1].name_size
-	 && !strcmp (img_info_list[i].name, img_info_list[i + 1].name))
+    for (j = i + 1; j < ((obey_order_flag == TRUE) ? i + 2 : img_info_size); ++j)
+    if ((img_info_list[i].name_size == img_info_list[j].name_size
+	 && !strcmp (img_info_list[i].name, img_info_list[j].name))
 #if defined(__CYGWIN__) || defined(__MSYS__)
 	|| !strcmp (img_info_list[i].name, CYGWIN_DLL)
 #endif
        )
       {
 	free (img_info_list[i].name);
-	memmove (img_info_list + i, img_info_list + i + 1,
+	memmove (img_info_list + i, img_info_list + j,
 		 (img_info_size - i - 1) * sizeof (img_info_t));
 	--img_info_size;
 	--i;
+	--j;
       }
+}
+
+int
+merge_image_info ()
+{
+  int i, end;
+  img_info_t *match;
+  ULONG64 floating_image_base;
+
+  dedupe_image_info ();
+
   /* Iterate through new files and see if they are already available in
      existing database. */
   if (img_info_rebase_start)
@@ -1196,8 +1225,13 @@
 	  break;
 	}
     }
-
-  if ((image_base == 0 && perform_rebase_flag && !image_storage_flag)
+#if defined(__CYGWIN__) || defined(__MSYS__)
+  if (image_base == 0)
+  {
+	  obey_order_flag = TRUE;
+  }
+#endif
+  if ((image_base == 0 && perform_rebase_flag && !image_storage_flag && !obey_order_flag)
       || (force_rebase_flag && !perform_rebase_flag))
     {
       usage ();
diff -urN rebase-4.4.1.orig/rebaseall.in rebase-4.4.1/rebaseall.in
--- rebase-4.4.1.orig/rebaseall.in	2014-06-14 14:11:24.073986700 +0100
+++ rebase-4.4.1/rebaseall.in	2014-06-14 14:11:36.750711700 +0100
@@ -29,7 +29,7 @@
 PATH=$(cd $tp2 && pwd):@bindir@:/bin
 
 ProgramName=${0##*/}
-ProgramOptions='48b:o:ps:tT:v'
+ProgramOptions='48b:io:ps:tT:v'
 DefaultBaseAddress=0x70000000
 DefaultOffset=@DEFAULT_OFFSET_VALUE@
 DefaultTouch=
@@ -37,17 +37,18 @@
 DefaultVerbose=
 DefaultFileList=
 DefaultSuffixes='dll|so|oct'
+DatabaseFlag=-s
 
 # Define functions
 usage()
 {
-    echo "usage: ${ProgramName} [-b BaseAddress] [-o Offset] [-s DllSuffix] [-T FileList | -] [-4|-8] [-p] [-t] [-v]"
+    echo "usage: ${ProgramName} [-b BaseAddress] [-o Offset] [-s DllSuffix] [-T FileList | -] [-4|-8] [-p] [-t] [-i] [-v]"
     exit 1
 }
 
 cleanup()
 {
-    rm -f "${TmpFile}" "${SortedFile}"
+    rm -f "${TmpFile}"
     exit ${ExitCode}
 }
 
@@ -121,6 +122,8 @@
     	Touch="-t";;
     T)
 	FileList="${OPTARG}";;
+    i)
+	DatabaseFlag=;;
     v)
 	Verbose="-v";;
     \?)
@@ -175,8 +178,8 @@
 [ -f "${db_file}" ] && database_exists="yes"
 
 # If BaseAddress has not been specified, and the rebase database doesn't exist
-# yet, set BaseAddress to default.
-if [ -z "${BaseAddress}" -a "${database_exists}" != "yes" ]
+# yet, set BaseAddress to default, unless ignore database has been specified.
+if [ -z "${BaseAddress}" -a "${database_exists}" != "yes" -a -n "${DatabaseFlag}" ]
 then
   BaseAddress=$DefaultBaseAddress
 fi
@@ -204,8 +207,15 @@
 fi
 
 # Set temp file
-SortedFile="$TmpDir/rebase.lst"
-TmpFile="${SortedFile}.in"
+TmpFile="$TmpDir/rebase.lst"
+# Prepend user supplied file list, if any
+if [ -n "${FileList}" ]
+then
+    cat "${FileList}" >"${TmpFile}"
+else
+    [ -f "${TmpFile}" ] && rm -f "${TmpFile}"
+    touch "${TmpFile}"
+fi
 
 # Create rebase list
 case $Platform in
@@ -214,7 +224,7 @@
       grep -E "\.($Suffixes)\$" |
       sed -e '/\/cygwin1\.dll$/d' -e '/\/cyglsa.*\.dll$/d' \
           -e '/sys-root\/mingw/d' -e 's/^/\//' \
-          -e '/\/d\?ash\.exe$/d' -e '/\/rebase\.exe$/d' >"${TmpFile}"
+          -e '/\/d\?ash\.exe$/d' -e '/\/rebase\.exe$/d' >>"${TmpFile}"
     # some interpreters include a method for installing addons outside of the
     # package manager, such as CPAN and RubyGems.
     for d in /usr/lib/perl5/site_perl /usr/lib/py*/site-packages \
@@ -257,20 +267,11 @@
     ;;
 esac
 
-# Append user supplied file list, if any
-if [ -n "${FileList}" ]
-then
-    cat "${FileList}" >>"${TmpFile}"
-fi
-
-# Remove duplicates
-sort -u "${TmpFile}" > "${SortedFile}"
-
 if [ -z "${BaseAddress}" ]
 then
-  rebase "${Verbose}" "${Touch}" "${NoDyn}" -s "${Mach}" -T "${SortedFile}"
+  rebase "${Verbose}" "${Touch}" "${NoDyn}" "${DatabaseFlag}" "${Mach}" -T "${TmpFile}"
 else
-  rebase "${Verbose}" "${Touch}" "${NoDyn}" -s "${Mach}" -b "${BaseAddress}" -o "${Offset}" -T "${SortedFile}"
+  rebase "${Verbose}" "${Touch}" "${NoDyn}" "${DatabaseFlag}" "${Mach}" -b "${BaseAddress}" -o "${Offset}" -T "${TmpFile}"
 fi
 ExitCode=$?