FIX: for Windows users, it seems logical to favor native win32 installation before Cygwin ones. Otherwise you can end up with bad mixes (part of the java tools were picked from the SDK, part from Cygwin)

Modules/CMakeDetermineJavaCompiler.cmake

@@ -29,13 +29,13 @@ IF(NOT CMAKE_JAVA_COMPILER)
   ENDIF($ENV{JAVA_ARCHIVE} MATCHES ".+")
 
   SET(JAVA_BIN_PATH
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/bin"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/bin"
     /usr/bin
     /usr/lib/java/bin
     /usr/share/java/bin
     /usr/local/bin
     /usr/local/java/bin
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/bin"
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/bin"
     )
   # if no compiler has been specified yet, then look for one
   IF(CMAKE_JAVA_COMPILER_INIT)

Modules/FindJNI.cmake

@@ -9,21 +9,21 @@
 # 
 
 SET(JAVA_AWT_LIBRARY_DIRECTORIES
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/lib"
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/lib"
   /usr/lib
   /usr/local/lib
   /usr/lib/java/jre/lib/i386
   /usr/local/lib/java/jre/lib/i386
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/lib"
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/lib"
   )
 
 SET(JAVA_AWT_INCLUDE_DIRECTORIES
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/include"
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/include"
   /usr/include 
   /usr/local/include
   /usr/lib/java/include
   /usr/local/lib/java/include
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/include"
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/include"
   )
 
 IF(APPLE)

Modules/FindJava.cmake

@@ -9,13 +9,13 @@
 #
 
 SET(JAVA_BIN_PATH
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/bin"
+  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/bin"
   /usr/bin
   /usr/lib/java/bin
   /usr/share/java/bin
   /usr/local/bin
   /usr/local/java/bin
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/bin"
-  "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/bin"
   )
 FIND_PROGRAM(JAVA_RUNTIME
   NAMES java

Modules/FindTCL.cmake

@@ -28,14 +28,14 @@ GET_FILENAME_COMPONENT(TK_WISH_PATH ${TK_WISH} PATH)
 SET (TCLTK_POSSIBLE_LIB_PATHS
   "${TCL_TCLSH_PATH}/../lib"
   "${TK_WISH_PATH}/../lib"
-  /usr/lib 
-  /usr/local/lib
   "C:/Program Files/Tcl/lib" 
   "C:/Tcl/lib" 
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.4;Root]/lib
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.3;Root]/lib
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.2;Root]/lib
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.0;Root]/lib
+  /usr/lib 
+  /usr/local/lib
 )
 
 FIND_LIBRARY(TCL_LIBRARY
@@ -87,18 +87,18 @@ SET (TCLTK_POSSIBLE_INCLUDE_PATHS
   /Library/Frameworks/Tk.framework/PrivateHeaders
   "${TCL_TCLSH_PATH}/../include"
   "${TK_WISH_PATH}/../include"
-  /usr/include 
-  /usr/local/include
-  /usr/include/tcl8.4
-  /usr/include/tcl8.3
-  /usr/include/tcl8.2
-  /usr/include/tcl8.0
   "C:/Program Files/Tcl/include" 
   "C:/Tcl/include" 
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.4;Root]/include
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.3;Root]/include
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.2;Root]/include
   [HKEY_LOCAL_MACHINE\\SOFTWARE\\Scriptics\\Tcl\\8.0;Root]/include
+  /usr/include 
+  /usr/local/include
+  /usr/include/tcl8.4
+  /usr/include/tcl8.3
+  /usr/include/tcl8.2
+  /usr/include/tcl8.0
 )
 
 FIND_PATH(TCL_INCLUDE_PATH tcl.h