diff --git a/README b/README
index 86a016433..bc70780a8 100644
--- a/README
+++ b/README
@@ -67,6 +67,14 @@ make
 
 
 TODO:
-configure stuff for windows should be a copy configure file
-read in depend regular expression from a file
+
+
+Add include and directories to the build on windows.
+For unix just add them to the CMakeLocal.make.in
+
+Add a --with idea, sets a #define in the config.h file
+
+Change ME to LIBRARY, and add PROJECT=
+
+
 
diff --git a/Source/CMakeBuildTargets.cxx b/Source/CMakeBuildTargets.cxx
index 0da141078..eea02d952 100644
--- a/Source/CMakeBuildTargets.cxx
+++ b/Source/CMakeBuildTargets.cxx
@@ -2,6 +2,9 @@
 #include "cmMakeDepend.h"
 #include <iostream>
 
+
+// This is the main program used to gentrate makefile fragments 
+// from CMakeLists.txt input files.   
 main(int ac, char** av)
 {
   if(ac < 2)
@@ -9,38 +12,46 @@ main(int ac, char** av)
     std::cerr << "Usage: " << av[0] << " Makefile.in  -Ipath ..." << std::endl;
     return -1;
     }
-  cmUnixMakefile* mf = new cmUnixMakefile;
+  // Create a unix makefile
+  cmUnixMakefile mf;
+  // Create a depends object
   cmMakeDepend md;
+  // Parse the command line
   if(ac > 2)
     {
     for(int i =2; i < ac; i++)
       {
       std::string arg = av[i];
+      // Set the current source directory with a -S dir options
       if(arg.find("-S",0) != std::string::npos)
 	{
 	std::string path = arg.substr(2);
-	mf->SetCurrentDirectory(path.c_str());
+	mf.SetCurrentDirectory(path.c_str());
 	}
+      // Set the output or binary directory with a -B dir option
       if(arg.find("-B",0) != std::string::npos)
 	{
 	std::string path = arg.substr(2);
-	mf->SetOutputHomeDirectory(path.c_str());
+	mf.SetOutputHomeDirectory(path.c_str());
 	}
+      // Set the source home directory with a -H dir option
       if(arg.find("-H",0) != std::string::npos)
 	{
 	std::string path = arg.substr(2);
-	mf->SetHomeDirectory(path.c_str());
+	mf.SetHomeDirectory(path.c_str());
 	}
       }
     }
-  if(!mf->ReadMakefile(av[1]))
+  // Read and parse the input makefile
+  if(!mf.ReadMakefile(av[1]))
     {
     std::cerr << "Usage: " << av[0] << " Makefile.in  -Ipath ..." << std::endl;
     return -1;
     }
-
-  md.SetMakefile(mf);
+  // Set the makefile object on the depend object
+  md.SetMakefile(&mf);
+  // compute the depend information
   md.DoDepends();
-  mf->OutputMakefile("CMakeTargets.make");
-  delete mf;
+  // Ouput the result
+  mf.OutputMakefile("CMakeTargets.make");
 }
diff --git a/Source/CMakeSetupCMD.cxx b/Source/CMakeSetupCMD.cxx
index 4ffd20c0f..8e6432479 100644
--- a/Source/CMakeSetupCMD.cxx
+++ b/Source/CMakeSetupCMD.cxx
@@ -2,6 +2,12 @@
 #include "cmDSPMakefile.h"
 #include <iostream>
 
+// this is the command line version of CMakeSetup.
+// It is called from Visual Studio when a CMakeLists.txt
+// file is changed.
+
+
+// Set the command line arguments
 void SetArgs(cmMakefile& builder, int ac, char** av)
 {
   for(int i =3; i < ac; i++)
@@ -32,10 +38,9 @@ void SetArgs(cmMakefile& builder, int ac, char** av)
     }
 }
 
+
 main(int ac, char** av)
 {
-  std::cerr << "pcbuilderCMD\n ";
-  
   if(ac < 3)
     {
     std::cerr << "Usage: " << av[0] << 
diff --git a/Source/cmCollectFlags.cxx b/Source/cmCollectFlags.cxx
index c936718f0..6e7e33cd8 100644
--- a/Source/cmCollectFlags.cxx
+++ b/Source/cmCollectFlags.cxx
@@ -1,4 +1,5 @@
 #include "cmCollectFlags.h"
+#include "cmMakefile.h"
 #include "cmSystemTools.h"
 #include <fstream>
 #include <iterator>
@@ -107,3 +108,32 @@ void cmCollectFlags::ParseDirectory(const char* dir)
     this->ParseDirectory(dotdotDir.c_str());
     }
 }
+
+
+// expance CMAKE_BINARY_DIR and CMAKE_SOURCE_ROOT in the
+// include and library directories.
+
+void cmCollectFlags::ExpandVaribles(cmMakefile* makefile)
+{
+   // Now replace varibles
+  std::vector<std::string>& includes = m_IncludeDirectories;
+  std::vector<std::string>::iterator j, begin, end;
+  begin = m_IncludeDirectories.begin();
+  end = m_IncludeDirectories.end();
+  for(j = begin; j != end; ++j)
+    {
+    cmSystemTools::ReplaceString(*j, "${CMAKE_BINARY_DIR}",
+				 makefile->GetOutputHomeDirectory() );
+    cmSystemTools::ReplaceString(*j, "${CMAKE_SOURCE_ROOT}",
+				 makefile->GetHomeDirectory() );
+    }
+  begin = m_LinkDirectories.begin();
+  end = m_LinkDirectories.end();
+  for(j = begin; j != end; ++j)
+    {
+    cmSystemTools::ReplaceString(*j, "${CMAKE_BINARY_DIR}",
+				 makefile->GetOutputHomeDirectory() );
+    cmSystemTools::ReplaceString(*j, "${CMAKE_SOURCE_ROOT}",
+				 makefile->GetHomeDirectory() );
+    }
+}
diff --git a/Source/cmCollectFlags.h b/Source/cmCollectFlags.h
index 8f037da96..28448b117 100644
--- a/Source/cmCollectFlags.h
+++ b/Source/cmCollectFlags.h
@@ -15,12 +15,16 @@
 =========================================================================*/
 /**
  * cmCollectFlags - collect flags from CMakeLists.txt files.
+ * This class collects include and link flags from a CMakeLists.txt
+ * file and any CMakeLists.txt files above it in the directory tree.
+ * It stops searching wen the home directory is found.
  */
 #ifndef cmCollectFlags_h
 #define cmCollectFlags_h
 
 #include <vector>
 #include <string>
+class cmMakefile;
 
 class cmCollectFlags
 {
@@ -45,6 +49,13 @@ public:
    */
   void Print();
   
+  /**
+   * Expance varibles for home and binary root in the collected flags.
+   * CMAKE_BINARY_DIR and CMAKE_SOURCE_ROOT are replaced with
+   * makefile->GetOutputHomeDirectory() and
+   * makefile->GetHomeDirectory()
+   */
+  void ExpandVaribles(cmMakefile* makefile);
   
   std::vector<std::string>& GetIncludeDirectories()
     { 
diff --git a/Source/cmDSPMakefile.cxx b/Source/cmDSPMakefile.cxx
index 3fa6c0622..9147bcbcf 100644
--- a/Source/cmDSPMakefile.cxx
+++ b/Source/cmDSPMakefile.cxx
@@ -16,17 +16,13 @@ static void Die(const char* message)
 
 void cmDSPMakefile::OutputDSPFile()
 { 
+  // Setup /I and /LIBPATH options
   std::vector<std::string>& includes = m_BuildFlags.GetIncludeDirectories();
   std::vector<std::string>::iterator i;
   for(i = includes.begin(); i != includes.end(); ++i)
     {
-    std::string include = *i;
-    cmSystemTools::ReplaceString(include, "${CMAKE_BINARY_DIR}",
-				 this->GetOutputHomeDirectory() );
-    cmSystemTools::ReplaceString(include, "${CMAKE_SOURCE_ROOT}",
-				 this->GetHomeDirectory() );
     m_IncludeOptions +=  "/I \"";
-    m_IncludeOptions += include;
+    m_IncludeOptions += *i;
     m_IncludeOptions += "\" ";
     }
   std::vector<std::string>& libs = m_BuildFlags.GetLinkLibraries();
@@ -48,8 +44,6 @@ void cmDSPMakefile::OutputDSPFile()
     {
     m_DebugLibraryOptions += " /LIBPATH:\"";
     m_DebugLibraryOptions += *i;
-    cmSystemTools::ReplaceString(m_DebugLibraryOptions, "${CMAKE_BINARY_DIR}",
-				 this->GetOutputHomeDirectory() );
     if(i->find("Debug") == std::string::npos)
       {
       if(i->find("Release") == std::string::npos)
diff --git a/Source/cmDSPWriter.cxx b/Source/cmDSPWriter.cxx
index 3fa6c0622..9147bcbcf 100644
--- a/Source/cmDSPWriter.cxx
+++ b/Source/cmDSPWriter.cxx
@@ -16,17 +16,13 @@ static void Die(const char* message)
 
 void cmDSPMakefile::OutputDSPFile()
 { 
+  // Setup /I and /LIBPATH options
   std::vector<std::string>& includes = m_BuildFlags.GetIncludeDirectories();
   std::vector<std::string>::iterator i;
   for(i = includes.begin(); i != includes.end(); ++i)
     {
-    std::string include = *i;
-    cmSystemTools::ReplaceString(include, "${CMAKE_BINARY_DIR}",
-				 this->GetOutputHomeDirectory() );
-    cmSystemTools::ReplaceString(include, "${CMAKE_SOURCE_ROOT}",
-				 this->GetHomeDirectory() );
     m_IncludeOptions +=  "/I \"";
-    m_IncludeOptions += include;
+    m_IncludeOptions += *i;
     m_IncludeOptions += "\" ";
     }
   std::vector<std::string>& libs = m_BuildFlags.GetLinkLibraries();
@@ -48,8 +44,6 @@ void cmDSPMakefile::OutputDSPFile()
     {
     m_DebugLibraryOptions += " /LIBPATH:\"";
     m_DebugLibraryOptions += *i;
-    cmSystemTools::ReplaceString(m_DebugLibraryOptions, "${CMAKE_BINARY_DIR}",
-				 this->GetOutputHomeDirectory() );
     if(i->find("Debug") == std::string::npos)
       {
       if(i->find("Release") == std::string::npos)
diff --git a/Source/cmDSWMakefile.cxx b/Source/cmDSWMakefile.cxx
index 271bd3ead..5ce7b2c18 100644
--- a/Source/cmDSWMakefile.cxx
+++ b/Source/cmDSWMakefile.cxx
@@ -12,7 +12,7 @@
 #undef GetCurrentDirectory
 #undef SetCurrentDirectory
 
-// virtual override, ouput the makefile 
+// output the DSW file
 void cmDSWMakefile::OutputDSWFile()
 { 
   if(m_OutputDirectory == "")
diff --git a/Source/cmDSWWriter.cxx b/Source/cmDSWWriter.cxx
index 271bd3ead..5ce7b2c18 100644
--- a/Source/cmDSWWriter.cxx
+++ b/Source/cmDSWWriter.cxx
@@ -12,7 +12,7 @@
 #undef GetCurrentDirectory
 #undef SetCurrentDirectory
 
-// virtual override, ouput the makefile 
+// output the DSW file
 void cmDSWMakefile::OutputDSWFile()
 { 
   if(m_OutputDirectory == "")
diff --git a/Source/cmMakeDepend.cxx b/Source/cmMakeDepend.cxx
index d6841606a..8499d87b1 100644
--- a/Source/cmMakeDepend.cxx
+++ b/Source/cmMakeDepend.cxx
@@ -48,10 +48,6 @@ void cmMakeDepend::SetMakefile(cmMakefile* makefile)
   std::vector<std::string>::iterator j;
   for(j = includes.begin(); j != includes.end(); ++j)
     {
-    cmSystemTools::ReplaceString(*j, "${CMAKE_BINARY_DIR}",
-				 m_Makefile->GetOutputHomeDirectory() );
-    cmSystemTools::ReplaceString(*j, "${CMAKE_SOURCE_ROOT}",
-				 m_Makefile->GetHomeDirectory() );
     this->AddSearchPath(j->c_str());
     }
   // Now create cmDependInformation objects for files in the directory
diff --git a/Source/cmMakefile.cxx b/Source/cmMakefile.cxx
index 3fa59a98e..1b6538c8e 100644
--- a/Source/cmMakefile.cxx
+++ b/Source/cmMakefile.cxx
@@ -24,13 +24,13 @@ void cmMakefile::Print()
 }
 
 // Parse the given CMakeLists.txt file into a list of classes.
-
 bool cmMakefile::ReadMakefile(const char* filename)
 {
   m_BuildFlags.SetSourceHomeDirectory(this->GetHomeDirectory());
   m_BuildFlags.SetStartDirectory(this->GetCurrentDirectory());
   m_BuildFlags.ParseDirectories();
-
+  m_BuildFlags.ExpandVaribles(this);
+ 
   std::ifstream fin(filename);
   if(!fin)
     {
@@ -188,11 +188,12 @@ void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
   std::string::size_type start = line.find("=");
   if(start != std::string::npos)
     {
-    std::string dirname = line.substr(start+1, line.size());
-    dirname = cmSystemTools::CleanUpName(dirname.c_str());
+    std::string templateDirectory = line.substr(start+1, line.size());
+    templateDirectory = cmSystemTools::CleanUpName(templateDirectory.c_str());
+    m_TemplateDirectories.push_back(templateDirectory);
     std::string tdir = this->GetCurrentDirectory();
     tdir += "/";
-    tdir += dirname;
+    tdir += templateDirectory;
     // Load all the files in the directory
     cmDirectory dir;
     if(dir.Load(tdir.c_str()))
@@ -207,7 +208,7 @@ void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
           // Remove the extension
           std::string::size_type dotpos = file.rfind(".");
           file = file.substr(0, dotpos);
-          std::string fullname = dirname;
+          std::string fullname = templateDirectory;
           fullname += "/";
           fullname += file;
           // add the file as a class file so 
@@ -221,8 +222,8 @@ void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
       }
     else
       {
-      std::cerr << "Error can not open template instance directory "
-                << dirname.c_str() << std::endl;
+      std::cerr << "Warning can not open template instance directory "
+                << templateDirectory.c_str() << std::endl;
       }
     }
 }
diff --git a/Source/cmMakefile.h b/Source/cmMakefile.h
index 94cb988ab..3396dd5fb 100644
--- a/Source/cmMakefile.h
+++ b/Source/cmMakefile.h
@@ -101,6 +101,7 @@ private:
 protected:
   bool m_Executables;
   std::string m_Prefix;
+  std::vector<std::string> m_TemplateDirectories; // Template directory name if found in file
   std::string m_OutputDirectory; // Current output directory for makefile
   std::string m_OutputHomeDirectory; // Top level output directory
   std::string m_cmHomeDirectory; // Home directory for source
diff --git a/Source/cmUnixMakefile.cxx b/Source/cmUnixMakefile.cxx
index a5d9b67c4..8a212959e 100644
--- a/Source/cmUnixMakefile.cxx
+++ b/Source/cmUnixMakefile.cxx
@@ -4,7 +4,8 @@
 #include <iostream>
 
 // Output the depend information for all the classes 
-// in the makefile.
+// in the makefile.  These would have been generated
+// by the class cmMakeDepend in the main of CMakeBuildTargets.
 void cmUnixMakefile::OutputDepends(std::ostream& fout)
 {
   for(int i = 0; i < m_Classes.size(); i++)
@@ -64,6 +65,18 @@ inline std::string FixDirectoryName(const char* dir)
 
 void cmUnixMakefile::OutputMakefile(const char* file)
 {
+  if( m_TemplateDirectories.size() )
+    {
+    // For the case when this is running as a remote build
+    // on unix, make the directory
+    
+    for(std::vector<std::string>::iterator i = m_TemplateDirectories.begin();
+        i != m_TemplateDirectories.end(); ++i)
+      {
+      cmSystemTools::MakeDirectory(i->c_str());
+      }
+    }
+  
   std::ofstream fout(file);
   if(!fout)
     {
@@ -144,8 +157,6 @@ void cmUnixMakefile::OutputMakefile(const char* file)
       linkLibs += " ";
       }
     linkLibs += " ${LOCAL_LINK_FLAGS} ";
-    cmSystemTools::ReplaceString(linkLibs, "${CMAKE_BINARY_DIR}",
-				 this->GetOutputHomeDirectory() );
     // Now create rules for all of the executables to be built
     for(int i = 0; i < m_Classes.size(); i++)
       {
diff --git a/Source/itkVC60Configure.cxx b/Source/itkVC60Configure.cxx
deleted file mode 100644
index 498e30fe5..000000000
--- a/Source/itkVC60Configure.cxx
+++ /dev/null
@@ -1,57 +0,0 @@
-#include "itkVC60Configure.h"
-#include "cmSystemTools.h"
-#include "stdlib.h"
-#include <windows.h>
-
-void itkVC60Configure::Configure()
-{
-  this->GenerateITKConfigHeader();
-  this->GenerateVNLConfigHeader();
-}
-
-void itkVC60Configure::GenerateITKConfigHeader()
-{
-  // for now just copy the itkConfigure.h.in file into place
-  std::string source = m_WhereSource;
-  source += "/itkConfigure.h.in";
-  std::string destdir = m_WhereBuild;
-  std::string dest = destdir;
-  dest += "/itkConfigure.h";
-  this->CopyFileTo(source.c_str(),
-                   destdir.c_str(),
-                   dest.c_str());
-}
-
-void itkVC60Configure::CopyFileTo(const char* source,
-                                  const char* destdir,
-                                  const char* dest)
-{
-  if(!cmSystemTools::MakeDirectory(destdir) )
-    {
-    std::string error = "Error: can not create directory: ";
-    error += destdir;
-    MessageBox(0, error.c_str(), "config ERROR", MB_OK);
-    }
-  if(!CopyFile(source, dest, FALSE))
-    {
-     std::string error = "Error: can not create : ";
-     error += dest;
-     MessageBox(0, error.c_str(), "config ERROR", MB_OK);
-    }
-}
-
-
-void itkVC60Configure::GenerateVNLConfigHeader()
-{
-  // Copy the vcl config stuff for vc50 into place
-  std::string source = m_WhereSource;
-  source += "/Code/Insight3DParty/vxl/vcl/vcl_config-vc60.h ";
-  std::string destdir = m_WhereBuild;
-  destdir += "/Code/Insight3DParty/vxl/vcl";
-  std::string dest = destdir;
-  dest += "/vcl_config.h";
-  this->CopyFileTo(source.c_str(),
-                   destdir.c_str(),
-                   dest.c_str());
-  
-}
diff --git a/Source/itkVC60Configure.h b/Source/itkVC60Configure.h
deleted file mode 100644
index a30c71eb2..000000000
--- a/Source/itkVC60Configure.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*=========================================================================
-
-  Program:   Insight Segmentation & Registration Toolkit
-  Module:    $RCSfile$
-  Language:  C++
-  Date:      $Date$
-  Version:   $Revision$
-
-
-  Copyright (c) 2000 National Library of Medicine
-  All rights reserved.
-
-  See COPYRIGHT.txt for copyright details.
-
-=========================================================================*/
-/**
- * itkVC60Configure : a class that configures itk for build
- * on windows with VC60
- */
-#ifndef itkVC60Configure_h
-#define itkVC60Configure_h
-
-#include "cmWindowsConfigure.h"
-
-class itkVC60Configure : public cmWindowsConfigure
-{
-public:
-  /** 
-   * implement configure from parent
-   */
-  virtual void Configure();
-  /**
-   * create the main itk configure file
-   */
-  virtual void GenerateITKConfigHeader();
-  /**
-   * Create the vnl configure file
-   */
-  virtual void GenerateVNLConfigHeader();
-protected:
-  void CopyFileTo(const char* source,
-                  const char* destdir,
-                  const char* dest);
-};
-
-#endif