clarified cygwin/isabelle scripts;

--- a/Admin/Windows/Cygwin/init.bat	Thu Jan 10 17:53:15 2013 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-@echo off
-
-cd "%~dp0"
-cd "..\.."
-
-set CYGWIN=nodosfilewarning
-
-echo Initializing Cygwin ...
-"cygwin\bin\ash" /bin/rebaseall -p
-"cygwin\bin\bash" -c "PATH=/bin; bash -c 'source /etc/postinstall/base-files-mketc.sh.done'; mkpasswd -l >/etc/passwd; mkgroup -l >/etc/group"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Admin/Windows/Cygwin/isabelle/init.bat	Thu Jan 10 19:07:44 2013 +0100
@@ -0,0 +1,11 @@
+@echo off
+
+cd "%~dp0"
+cd "..\.."
+
+set CYGWIN=nodosfilewarning
+
+echo Initializing Cygwin ...
+"cygwin\bin\dash" /isabelle/rebaseall contrib/polyml-5.5.0
+"cygwin\bin\bash" /isabelle/postinstall
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Admin/Windows/Cygwin/isabelle/postinstall	Thu Jan 10 19:07:44 2013 +0100
@@ -0,0 +1,8 @@
+#!/bin/dash
+
+PATH=/bin
+
+bash /etc/postinstall/base-files-mketc.sh.done
+
+mkpasswd -l >/etc/passwd
+mkgroup -l >/etc/group

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Admin/Windows/Cygwin/isabelle/rebaseall	Thu Jan 10 19:07:44 2013 +0100
@@ -0,0 +1,14 @@
+#!/bin/dash
+
+PATH=/bin
+
+FILE_LIST="$(mktemp)"
+
+for DIR in "$@"
+do
+  find "$DIR" -name "*.dll" >> "$FILE_LIST"
+done
+
+dash /bin/rebaseall -T "$FILE_LIST"
+
+rm -f "$FILE_LIST"

--- a/Admin/lib/Tools/makedist_cygwin	Thu Jan 10 17:53:15 2013 +0100
+++ b/Admin/lib/Tools/makedist_cygwin	Thu Jan 10 19:07:44 2013 +0100
@@ -66,4 +66,5 @@
 
 rm "$TARGET/Cygwin.bat"
 
-cp "$ISABELLE_HOME/Admin/Windows/Cygwin/init.bat" "$TARGET/isabelle/."
+cp -a "$ISABELLE_HOME/Admin/Windows/Cygwin/isabelle/." "$TARGET/isabelle/."
+