ENH: CMake and configure now use SUBDIRS in CMakeLists.txt to find all the directories of the system.

38 files changed, 716 insertions, 916 deletions

diff --git a/CMakeMaster.make.in b/CMakeMaster.make.in
index 51aad8f..8d477c9 100644
--- a/CMakeMaster.make.in
+++ b/CMakeMaster.make.in
@@ -4,14 +4,14 @@
 
 #------------------------------------------------------------------------------
 # Include all variable settings
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeVariables.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeVariables.make@MAKEQUOTE@
 
 #------------------------------------------------------------------------------
 # Include user-editable defines.
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMakeLocal.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMakeLocal.make@MAKEQUOTE@
 
 #------------------------------------------------------------------------------
 # Include General Build Rules
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeRules.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeRules.make@MAKEQUOTE@
 
 
diff --git a/CMakeRules.make.in b/CMakeRules.make.in
index 91341f7..af10d2e 100644
--- a/CMakeRules.make.in
+++ b/CMakeRules.make.in
@@ -1,5 +1,5 @@
-# include simple rules for building .o files
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeSimpleRules.make@MAKEQUOTE@
+# include simple rules for building .o files from source files
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeSimpleRules.make@MAKEQUOTE@
 
 #
 # Makefile for 
@@ -10,18 +10,18 @@ all: CMakeTargets.make ${OBJ_SUB_DIRS} ${EXECUTABLES} ${SUBDIR_BUILD} ${BUILD_LI
 
 #------------------------------------------------------------------------------
 
-${CMAKE}: @fullSrcDir@/CMake/Source/*.cxx @fullSrcDir@/CMake/Source/*.h
-	cd @CMAKE_OBJ_DIR@/CMake/Source; ${MAKE} CMakeBuildTargets
+${CMAKE}: ${topdir}/CMake/Source/*.cxx ${topdir}/CMake/Source/*.h
+	cd ${CMAKE_CONFIG_DIR}/CMake/Source; ${MAKE} CMakeBuildTargets
 
 depend: ${CMAKE}
-	${CMAKE} ${srcdir}/CMakeLists.txt -S${srcdir} -I${srcdir} ${INCLUDE_FLAGS}
+	${MAKE} -${MAKEFLAGS} CMakeTargets.make
 
 
 clean: ${SUBDIR_CLEAN}
 	rm -f ${SRC_OBJ} ${EXECUTABLES} 
 
 CMakeTargets.make: ${CMAKE} ${srcdir}/CMakeLists.txt
-	${CMAKE} ${srcdir}/CMakeLists.txt -S${srcdir} -I${srcdir} ${INCLUDE_FLAGS}
+	${CMAKE} ${srcdir}/CMakeLists.txt -S${srcdir} -H${topdir} -B${CMAKE_CONFIG_DIR}
 
 #------------------------------------------------------------------------------
 # rules for the normal library
diff --git a/CMakeTargets.make.in b/CMakeTargets.make.in
new file mode 100644
index 0000000..a9405ec
--- /dev/null
+++ b/CMakeTargets.make.in
@@ -0,0 +1,5 @@
+#empty file used by configure to generate initial targets.make files
+#if you find this as a make error, then the autoconf system is not
+#working, send for help on the insight mailing list...
+
+
diff --git a/CMakeVariables.make.in b/CMakeVariables.make.in
index 07a6f1a..a2b5eeb 100644
--- a/CMakeVariables.make.in
+++ b/CMakeVariables.make.in
@@ -1,11 +1,39 @@
+
+# ***** BEGIN VARIBLES THAT CAN BE OVERRIDDEN IN CMakeLocal.make.in **************
+# CMakeLocal.make.in should be in the directory where you run configure
+# in, which need not be the source directory
+
+# use this to add targets to the default all 
+# so they are built when make is run by default
+LOCAL_BUILD_TARGETS = 
+
+# use this flag to add -L and -l options to the link line
+LOCAL_LINK_FLAGS =
+
+# use this flag to add -I flags to the compile line
+LOCAL_INCLUDE_FLAGS =
+
+# use this flag to add compiler options like -g -O, etc
+# for the "C" compiler, for gcc these default to -g -O2
+USER_CFLAGS   = @CFLAGS@
+
+# use this flag to add compiler options like -g -O, etc
+# for the "C++" compiler, for gcc these default to -g -O2
+USER_CXXFLAGS = @CXXFLAGS@
+
+# ***** END VARIBLES THAT CAN BE OVERRIDDEN IN CMakeLocal.make.in **************
+
+
+# This is the path to the top of the Source tree
 topdir = @fullSrcDir@
 
-CONFIG_DIR = @CMAKE_OBJ_DIR@
+# This is the directory configure was run in
+# where the binaries will be placed
+CMAKE_CONFIG_DIR = @CMAKE_CONFIG_DIR@
 
+# the standard shell for make
 SHELL = /bin/sh
 
-CMAKE_OBJ_DIR = ${CONFIG_DIR}
-
 RANLIB        = @RANLIB@
 CC            = @CC@
 CFLAGS        = @ITK_SHLIB_CFLAGS@ @ANSI_CFLAGS@
@@ -82,31 +110,21 @@ LIB_INSTALL_DIR = $(INSTALL_ROOT)$(exec_prefix)/lib
 BIN_INSTALL_DIR = $(INSTALL_ROOT)$(exec_prefix)/bin
 
 # set up the path to the rulesgen program
-CMAKE = @CMAKE_OBJ_DIR@/CMake/Source/CMakeBuildTargets
+CMAKE = @CMAKE_CONFIG_DIR@/CMake/Source/CMakeBuildTargets
 KIT_OBJ =  ${SRC_OBJ} ${EXTRA_KIT_OBJ}
 
 
-# ***** BEGIN VARIBLES THAT CAN BE OVERRIDDEN IN CMakeLocal.make.in **************
 
-LOCAL_BUILD_TARGETS = 
-LOCAL_LINK_FLAGS =
-USER_CFLAGS   = @CFLAGS@
-USER_CXXFLAGS = @CXXFLAGS@
-
-# ***** END VARIBLES THAT CAN BE OVERRIDDEN IN CMakeLocal.make.in **************
 
-
-
-# compile line flags
-INCLUDE_FLAGS = -I. \
-	-I${CONFIG_DIR}/Code/Insight3DParty/vxl \
-	-I${CONFIG_DIR} \
-	-I${topdir}/Code/Common \
-	-I${topdir}/Code/Insight3DParty/vxl 
+# C++ compile flags, INCLUDE_FLAGS is set in CMakeTargets.make which
+# is generated by CMakeBuildTargets, see CMake/Source
 
 CXX_FLAGS = ${CPPFLAGS} ${USER_CXXFLAGS} ${CXXFLAGS} \
 	    ${KIT_FLAGS} ${INCLUDE_FLAGS}
 
-CC_FLAGS = ${CPPFLAGS} ${USER_CFLAGS} ${CFLAGS} 
+# C compile flags, INCLUDE_FLAGS is set in CMakeTargets.make which
+# is generated by CMakeBuildTargets, see CMake/Source
+
+CC_FLAGS = ${CPPFLAGS} ${USER_CFLAGS} ${CFLAGS} ${INCLUDE_FLAGS}
 
 
diff --git a/MakefileTemplate.in b/MakefileTemplate.in
index 0ce54fe..c02dc9a 100644
--- a/MakefileTemplate.in
+++ b/MakefileTemplate.in
@@ -1,4 +1,4 @@
 srcdir        = @srcdir@
 VPATH         = @srcdir@
 
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeMaster.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeMaster.make@MAKEQUOTE@
diff --git a/README b/README
index f913b56..f0f38a4 100644
--- a/README
+++ b/README
@@ -32,9 +32,11 @@ CMakeBuildTargets     -> Unix program to read CMakeLists.txt and generate CMakeT
 makefile fragments:
 CMakeMaster.make      -> main file to be included by makefiles
 CMakeVariables.make   -> all make varibles are set in this file
-CMakeRules.make       -> All build rules are here
+CMakeRules.make       -> All build rules are here (except Simple Rules)
+CMakeSimpleRules.make -> simple build rules for .o to .cxx, this is separate to be able
+to build CMakeBuildTargets itself.
 CMakeLocal.make       -> Place for hand configuration
-CMakeTargets.make     -> generated rules for make style build
+CMakeTargets.make     -> generated rules for make style build in each directory
 MakefileTemplate.make -> master makefile template used by configure to generate Makefiles
 
 Unix install:
@@ -50,7 +52,6 @@ make
 
 
 TODO:
-Fix cmUnixMakefile.cxx and cmDSPMakefile.cxx 
-to read libraries and -I stuff from a config file
-
+configure stuff for windows should be a copy configure file
+read in depend regular expression from a file
 
diff --git a/Source/CMakeBuildTargets.cxx b/Source/CMakeBuildTargets.cxx
index 06aebe8..0da1410 100644
--- a/Source/CMakeBuildTargets.cxx
+++ b/Source/CMakeBuildTargets.cxx
@@ -16,15 +16,20 @@ main(int ac, char** av)
     for(int i =2; i < ac; i++)
       {
       std::string arg = av[i];
-      if(arg.find("-I",0) != std::string::npos)
+      if(arg.find("-S",0) != std::string::npos)
 	{
 	std::string path = arg.substr(2);
-	md.AddSearchPath(path.c_str());
+	mf->SetCurrentDirectory(path.c_str());
 	}
-      if(arg.find("-S",0) != std::string::npos)
+      if(arg.find("-B",0) != std::string::npos)
 	{
 	std::string path = arg.substr(2);
-	mf->SetCurrentDirectory(path.c_str());
+	mf->SetOutputHomeDirectory(path.c_str());
+	}
+      if(arg.find("-H",0) != std::string::npos)
+	{
+	std::string path = arg.substr(2);
+	mf->SetHomeDirectory(path.c_str());
 	}
       }
     }
diff --git a/Source/CMakeSetup.cxx b/Source/CMakeSetup.cxx
deleted file mode 100644
index f01bcee..0000000
--- a/Source/CMakeSetup.cxx
+++ /dev/null
@@ -1,48 +0,0 @@
-#include "cmDSWBuilder.h"
-#include "cmDSPBuilder.h"
-#include <iostream>
-
-void SetArgs(cmPCBuilder& builder, int ac, char** av)
-{
-  for(int i =2; i < ac; i++)
-    {
-    std::string arg = av[i];
-    if(arg.find("-H",0) != std::string::npos)
-      {
-      std::string path = arg.substr(2);
-      builder.SetHomeDirectory(path.c_str());
-      }
-    if(arg.find("-D",0) != std::string::npos)
-      {
-      std::string path = arg.substr(2);
-      builder.SetCurrentDirectory(path.c_str());
-      }
-    }
-}
-
-main(int ac, char** av)
-{
-  if(ac < 3)
-    {
-    std::cerr << "Usage: " << av[0] << 
-      " Makefile.in -[DSP|DSW] -Hinsighthome -Dcurrentdir ..." << std::endl;
-    return -1;
-    }
-  std::string arg = av[2];
-  if(arg.find("-DSP", 0) != std::string::npos)
-    {
-    cmDSPBuilder builder;
-    builder.SetInputMakefilePath(av[1]);
-    SetArgs(builder, ac, av);
-    builder.CreateDSPFile();
-    }
-  else
-    {
-    cmDSWBuilder builder;
-    builder.SetInputMakefilePath(av[1]);
-    SetArgs(builder, ac, av);
-    builder.CreateDSWFile();
-    }
-  return 0;
-}
-
diff --git a/Source/CMakeSetup.dsw b/Source/CMakeSetup.dsw
index e04ca61..353ff46 100644
--- a/Source/CMakeSetup.dsw
+++ b/Source/CMakeSetup.dsw
@@ -12,9 +12,6 @@ Package=<5>
 Package=<4>

 {{{

     Begin Project Dependency

-    Project_Dep_Name pcbuilderCMD

-    End Project Dependency

-    Begin Project Dependency

     Project_Dep_Name CMakeSetupCMD

     End Project Dependency

 }}}

diff --git a/Source/CMakeSetupCMD.cxx b/Source/CMakeSetupCMD.cxx
index 46b2033..4ffd20c 100644
--- a/Source/CMakeSetupCMD.cxx
+++ b/Source/CMakeSetupCMD.cxx
@@ -1,8 +1,8 @@
-#include "cmDSWBuilder.h"
-#include "cmDSPBuilder.h"
+#include "cmDSWMakefile.h"
+#include "cmDSPMakefile.h"
 #include <iostream>
 
-void SetArgs(cmPCBuilder& builder, int ac, char** av)
+void SetArgs(cmMakefile& builder, int ac, char** av)
 {
   for(int i =3; i < ac; i++)
     {
@@ -16,7 +16,7 @@ void SetArgs(cmPCBuilder& builder, int ac, char** av)
       {
       std::string path = arg.substr(2);
       std::cerr << "set makefile dir " << path.c_str() << std::endl;
-      builder.SetMakefileDirectory(path.c_str());
+      builder.SetCurrentDirectory(path.c_str());
       }
     if(arg.find("-O",0) != std::string::npos)
       {
@@ -45,17 +45,17 @@ main(int ac, char** av)
   std::string arg = av[2];
   if(arg.find("-DSP", 0) != std::string::npos)
     {
-    cmDSPBuilder builder;
+    cmDSPMakefile builder;
     SetArgs(builder, ac, av);
-    builder.SetInputMakefilePath(av[1]);
-    builder.CreateDSPFile();
+    builder.ReadMakefile(av[1]);
+    builder.OutputDSPFile();
     }
   else
     {
-    cmDSWBuilder builder;
+    cmDSWMakefile builder;
     SetArgs(builder, ac, av);
-    builder.SetInputMakefilePath(av[1]);
-    builder.CreateDSWFile();
+    builder.ReadMakefile(av[1]);
+    builder.OutputDSWFile();
     }
   return 0;
 }
diff --git a/Source/CMakeSetupCMD.dsp b/Source/CMakeSetupCMD.dsp
index 9af6147..99992c9 100644
--- a/Source/CMakeSetupCMD.dsp
+++ b/Source/CMakeSetupCMD.dsp
@@ -99,6 +99,10 @@ SOURCE=.\cmClassFile.cxx
 # End Source File

 # Begin Source File

 

+SOURCE=.\cmCollectFlags.cxx

+# End Source File

+# Begin Source File

+

 SOURCE=.\cmDirectory.cxx

 # End Source File

 # Begin Source File

diff --git a/Source/MFCDialog/CMakeDialog.cpp b/Source/MFCDialog/CMakeDialog.cpp
deleted file mode 100644
index 373ad47..0000000
--- a/Source/MFCDialog/CMakeDialog.cpp
+++ /dev/null
@@ -1,327 +0,0 @@
-// CMakeSetupDialogDlg.cpp : implementation file
-//
-
-#include "stdafx.h"
-#include "pcbuilder.h"
-#include "CMakeSetupDialog.h"
-#include "../itkDSWBuilder.h"
-#include "../itkVC60Configure.h"
-
-#ifdef _DEBUG
-#define new DEBUG_NEW
-#undef THIS_FILE
-static char THIS_FILE[] = __FILE__;
-#endif
-
-/////////////////////////////////////////////////////////////////////////////
-// CAboutDlg dialog used for App About
-
-class CAboutDlg : public CDialog
-{
-public:
-  CAboutDlg();
-
-// Dialog Data
-  //{{AFX_DATA(CAboutDlg)
-  enum { IDD = IDD_ABOUTBOX };
-  //}}AFX_DATA
-
-  // ClassWizard generated virtual function overrides
-  //{{AFX_VIRTUAL(CAboutDlg)
-protected:
-  virtual void DoDataExchange(CDataExchange* pDX);    // DDX/DDV support
-  //}}AFX_VIRTUAL
-
-// Implementation
-protected:
-  //{{AFX_MSG(CAboutDlg)
-  //}}AFX_MSG
-  DECLARE_MESSAGE_MAP()
-    };
-
-CAboutDlg::CAboutDlg() : CDialog(CAboutDlg::IDD)
-{
-  //{{AFX_DATA_INIT(CAboutDlg)
-  //}}AFX_DATA_INIT
-}
-
-void CAboutDlg::DoDataExchange(CDataExchange* pDX)
-{
-  CDialog::DoDataExchange(pDX);
-  //{{AFX_DATA_MAP(CAboutDlg)
-  //}}AFX_DATA_MAP
-}
-
-BEGIN_MESSAGE_MAP(CAboutDlg, CDialog)
-  //{{AFX_MSG_MAP(CAboutDlg)
-  // No message handlers
-  //}}AFX_MSG_MAP
-  END_MESSAGE_MAP();
-
-
-/////////////////////////////////////////////////////////////////////////////
-// CMakeSetupDialog dialog
-
-CMakeSetupDialog::CMakeSetupDialog(CWnd* pParent /*=NULL*/)
-  : CDialog(CMakeSetupDialog::IDD, pParent)
-{
-  //{{AFX_DATA_INIT(CMakeSetupDialog)
-  m_WhereITK = _T("");
-  m_WhereBuildITK = _T("");
-  //}}AFX_DATA_INIT
-  // Note that LoadIcon does not require a subsequent DestroyIcon in Win32
-  m_hIcon = AfxGetApp()->LoadIcon(IDR_MAINFRAME);
-  m_WhereITK = _T("");
-  this->LoadFromRegistry();
-}
-
-void CMakeSetupDialog::DoDataExchange(CDataExchange* pDX)
-{
-  CDialog::DoDataExchange(pDX);
-  //{{AFX_DATA_MAP(CMakeSetupDialog)
-  DDX_Text(pDX, IDC_WhereITK, m_WhereITK);
-  DDX_Text(pDX, IDC_WhereITK2, m_WhereBuildITK);
-  //}}AFX_DATA_MAP
-}
-
-BEGIN_MESSAGE_MAP(CMakeSetupDialog, CDialog)
-  //{{AFX_MSG_MAP(CMakeSetupDialog)
-  ON_WM_SYSCOMMAND()
-  ON_WM_PAINT()
-  ON_WM_QUERYDRAGICON()
-  ON_EN_CHANGE(IDC_WhereITK, OnChangeEdit1)
-  ON_BN_CLICKED(IDC_BUTTON2, OnBrowse)
-  ON_BN_CLICKED(IDC_BUTTON3, OnButton3)
-  //}}AFX_MSG_MAP
-  END_MESSAGE_MAP();
-
-
-/////////////////////////////////////////////////////////////////////////////
-// CMakeSetupDialog message handlers
-
-BOOL CMakeSetupDialog::OnInitDialog()
-{
-  CDialog::OnInitDialog();
-
-  // Add "About..." menu item to system menu.
-
-  // IDM_ABOUTBOX must be in the system command range.
-  ASSERT((IDM_ABOUTBOX & 0xFFF0) == IDM_ABOUTBOX);
-  ASSERT(IDM_ABOUTBOX < 0xF000);
-
-  CMenu* pSysMenu = GetSystemMenu(FALSE);
-  if (pSysMenu != NULL)
-    {
-    CString strAboutMenu;
-    strAboutMenu.LoadString(IDS_ABOUTBOX);
-    if (!strAboutMenu.IsEmpty())
-      {
-      pSysMenu->AppendMenu(MF_SEPARATOR);
-      pSysMenu->AppendMenu(MF_STRING, IDM_ABOUTBOX, strAboutMenu);
-      }
-    }
-
-  // Set the icon for this dialog.  The framework does this automatically
-  //  when the application's main window is not a dialog
-  SetIcon(m_hIcon, TRUE);			// Set big icon
-  SetIcon(m_hIcon, FALSE);		// Set small icon
-	
-  // TODO: Add extra initialization here
-	
-  return TRUE;  // return TRUE  unless you set the focus to a control
-}
-
-void CMakeSetupDialog::OnSysCommand(UINT nID, LPARAM lParam)
-{
-  if ((nID & 0xFFF0) == IDM_ABOUTBOX)
-    {
-    CAboutDlg dlgAbout;
-    dlgAbout.DoModal();
-    }
-  else
-    {
-    CDialog::OnSysCommand(nID, lParam);
-    }
-}
-
-// If you add a minimize button to your dialog, you will need the code below
-//  to draw the icon.  For MFC applications using the document/view model,
-//  this is automatically done for you by the framework.
-
-void CMakeSetupDialog::OnPaint() 
-{
-  if (IsIconic())
-    {
-    CPaintDC dc(this); // device context for painting
-
-    SendMessage(WM_ICONERASEBKGND, (WPARAM) dc.GetSafeHdc(), 0);
-
-    // Center icon in client rectangle
-    int cxIcon = GetSystemMetrics(SM_CXICON);
-    int cyIcon = GetSystemMetrics(SM_CYICON);
-    CRect rect;
-    GetClientRect(&rect);
-    int x = (rect.Width() - cxIcon + 1) / 2;
-    int y = (rect.Height() - cyIcon + 1) / 2;
-
-    // Draw the icon
-    dc.DrawIcon(x, y, m_hIcon);
-    }
-  else
-    {
-    CDialog::OnPaint();
-    }
-}
-
-// The system calls this to obtain the cursor to display while the user drags
-//  the minimized window.
-HCURSOR CMakeSetupDialog::OnQueryDragIcon()
-{
-  return (HCURSOR) m_hIcon;
-}
-
-void CMakeSetupDialog::OnChangeEdit1() 
-{
-  // TODO: If this is a RICHEDIT control, the control will not
-  // send this notification unless you override the CDialog::OnInitDialog()
-  // function and call CRichEditCtrl().SetEventMask()
-  // with the ENM_CHANGE flag ORed into the mask.
-	
-  // TODO: Add your control notification handler code here
-	
-}
-
-void CMakeSetupDialog::OnBrowse() 
-{
-  this->UpdateData();
-  Browse(m_WhereITK, "Enter Path to Insight Source");
-  this->UpdateData(false);
-}
-
-bool CMakeSetupDialog::Browse(CString &result, const char *title)
-{
-// don't know what to do with initial right now...
-  char szPathName[4096];
-  BROWSEINFO bi;
- 
-  bi.hwndOwner = m_hWnd;
-  bi.pidlRoot = NULL;
-  bi.pszDisplayName = (LPTSTR)szPathName;
-  bi.lpszTitle = title;
-  bi.ulFlags = BIF_BROWSEINCLUDEFILES  ;
-  bi.lpfn = NULL;
-
-  LPITEMIDLIST pidl = SHBrowseForFolder(&bi);
-
-  bool bSuccess = (bool)SHGetPathFromIDList(pidl, szPathName);
-  if(bSuccess)
-    {
-    result = szPathName;
-    }
-  
-  return bSuccess;
-}
-
-void CMakeSetupDialog::OnOK() 
-{ 
-  // get all the info from the screen
-  this->UpdateData();
-  
-  // configure the system for VC60
-  itkVC60Configure config;
-  config.SetWhereITK(m_WhereITK);
-  config.SetWhereBuildITK(m_WhereBuildITK);
-  config.Configure();
-  
-  itkDSWBuilder builder;
-  // Set the ITK home directory
-  builder.SetHomeDirectory(m_WhereITK);
-  // Set the Makefile.in file
-  CString makefileIn = m_WhereITK;
-  makefileIn += "/Makefile.in";
-  builder.SetInputMakefilePath(makefileIn);
-  // Set the output directory
-  builder.SetOutputDirectory(m_WhereBuildITK);
-  // set the directory which contains the Makefile.in
-  builder.SetMakefileDirectory(m_WhereITK);
-  // Create the master DSW file and all children dsp files for ITK
-  builder.CreateDSWFile();
-  CDialog::OnOK();
-  this->SaveToRegistry();
-}
-
-void CMakeSetupDialog::OnButton3() 
-{
-  this->UpdateData();
-  Browse(m_WhereBuildITK, "Enter Path to Insight Build");
-  this->UpdateData(false);
-}
-
-void CMakeSetupDialog::SaveToRegistry()
-{ 
-  HKEY hKey;
-  DWORD dwDummy;
-
-  if(RegCreateKeyEx(HKEY_CURRENT_USER, 
-		    _T("Software\\Kitware\\ITK PCBuilder\\Settings"),
-		    0, "", REG_OPTION_NON_VOLATILE, KEY_READ|KEY_WRITE, 
-		    NULL, &hKey, &dwDummy) != ERROR_SUCCESS) 
-    {
-    return;
-    }
-  else
-    {
-    RegSetValueEx(hKey, _T("WhereITK"), 0, REG_SZ, 
-		  (CONST BYTE *)(const char *)m_WhereITK, 
-		  m_WhereITK.GetLength());
-    RegSetValueEx(hKey, _T("WhereBuildITK"), 0, REG_SZ, 
-		  (CONST BYTE *)(const char *)m_WhereBuildITK, 
-		  m_WhereBuildITK.GetLength());
-    
-    }
-  RegCloseKey(hKey);
-}
-
-
-void CMakeSetupDialog::ReadRegistryValue(HKEY hKey,
-					    CString *val,
-					    char *key,
-					    char *adefault)
-{
-  DWORD dwType, dwSize;
-  char *pb;
-
-  dwType = REG_SZ;
-  pb = val->GetBuffer(MAX_PATH);
-  dwSize = MAX_PATH;
-  if(RegQueryValueEx(hKey,_T(key), NULL, &dwType, 
-		     (BYTE *)pb, &dwSize) != ERROR_SUCCESS)
-    {
-    val->ReleaseBuffer();
-    *val = _T(adefault);
-    }
-  else
-    {
-    val->ReleaseBuffer();
-    }
-}
-
-
-void CMakeSetupDialog::LoadFromRegistry()
-{ 
-  HKEY hKey;
-  if(RegOpenKeyEx(HKEY_CURRENT_USER, 
-		  _T("Software\\Kitware\\ITK PCBuilder\\Settings"), 
-		  0, KEY_READ, &hKey) != ERROR_SUCCESS)
-    {
-    return;
-    }
-  else
-    {
-    // save some values
-    this->ReadRegistryValue(hKey, &(m_WhereITK),"WhereITK","C:\\Insight");
-    this->ReadRegistryValue(hKey, &(m_WhereBuildITK),"WhereBuildITK",
-			    "C:\\vtkbin");
-    }
-  RegCloseKey(hKey);
-}
diff --git a/Source/MFCDialog/CMakeSetup.dsp b/Source/MFCDialog/CMakeSetup.dsp
index 9864a7c..3e59357 100644
--- a/Source/MFCDialog/CMakeSetup.dsp
+++ b/Source/MFCDialog/CMakeSetup.dsp
@@ -108,6 +108,10 @@ SOURCE=..\cmClassFile.cxx
 # End Source File

 # Begin Source File

 

+SOURCE=..\cmCollectFlags.cxx

+# End Source File

+# Begin Source File

+

 SOURCE=..\cmDirectory.cxx

 # End Source File

 # Begin Source File

@@ -232,9 +236,5 @@ SOURCE=.\res\CMakeSetupDialog.ico
 SOURCE=.\res\CMakeSetupDialog.rc2

 # End Source File

 # End Group

-# Begin Source File

-

-SOURCE=.\ReadMe.txt

-# End Source File

 # End Target

 # End Project

diff --git a/Source/MFCDialog/CMakeSetupDialog.cpp b/Source/MFCDialog/CMakeSetupDialog.cpp
index 32b8027..f3dc17b 100644
--- a/Source/MFCDialog/CMakeSetupDialog.cpp
+++ b/Source/MFCDialog/CMakeSetupDialog.cpp
@@ -4,7 +4,7 @@
 #include "stdafx.h"
 #include "CMakeSetup.h"
 #include "CMakeSetupDialog.h"
-#include "../cmDSWBuilder.h"
+#include "../cmDSWMakefile.h"
 #include "../itkVC60Configure.h"
 
 #ifdef _DEBUG
@@ -232,19 +232,19 @@ void CMakeSetupDialog::OnOK()
   config.SetWhereBuild(m_WhereBuild);
   config.Configure();
   
-  cmDSWBuilder builder;
+  cmDSWMakefile builder;
   // Set the ITK home directory
   builder.SetHomeDirectory(m_WhereSource);
   // Set the CMakeLists.txt file
   CString makefileIn = m_WhereSource;
   makefileIn += "/CMakeLists.txt";
-  builder.SetInputMakefilePath(makefileIn);
+  builder.ReadMakefile(makefileIn);
   // Set the output directory
   builder.SetOutputDirectory(m_WhereBuild);
   // set the directory which contains the CMakeLists.txt
-  builder.SetMakefileDirectory(m_WhereSource);
+  builder.SetCurrentDirectory(m_WhereSource);
   // Create the master DSW file and all children dsp files for ITK
-  builder.CreateDSWFile();
+  builder.OutputDSWFile();
   CDialog::OnOK();
   this->SaveToRegistry();
 }
diff --git a/Source/Makefile.in b/Source/Makefile.in
index 0a51b1a..b9d5ca0 100644
--- a/Source/Makefile.in
+++ b/Source/Makefile.in
@@ -6,8 +6,8 @@ VPATH         = @srcdir@
 # This will cause an infinite loop as it will add the
 # rule for changing into this directory
 
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeVariables.make@MAKEQUOTE@
-@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_OBJ_DIR@/CMake/CMakeSimpleRules.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeVariables.make@MAKEQUOTE@
+@MAKEINCLUDE@ @MAKEQUOTE@@CMAKE_CONFIG_DIR@/CMake/CMakeSimpleRules.make@MAKEQUOTE@
 
 OBJS = \
 cmClassFile.o \
@@ -16,12 +16,16 @@ cmMakefile.o \
 cmUnixMakefile.o \
 cmMakeDepend.o \
 cmRegularExpression.o \
-CMakeBuildTargets.o 
+cmSystemTools.o \
+CMakeBuildTargets.o \
+cmCollectFlags.o
 
 
-cmDirectory.o : cmDirectory.h cmDirectory.cxx
-cmClassFile.o : cmClassFile.h cmClassFile.cxx
-cmMakefile.o : cmMakefile.h cmMakefile.cxx cmClassFile.h
+cmCollectFlags.o : cmCollectFlags.h cmCollectFlags.cxx cmSystemTools.h
+cmSystemTools.o : cmSystemTools.h cmSystemTools.cxx cmSystemTools.h
+cmDirectory.o : cmDirectory.h cmDirectory.cxx cmSystemTools.h
+cmClassFile.o : cmClassFile.h cmClassFile.cxx cmSystemTools.h
+cmMakefile.o : cmMakefile.h cmMakefile.cxx cmClassFile.h cmSystemTools.h
 cmUnixMakefile.o : cmUnixMakefile.h cmUnixMakefile.cxx cmMakefile.h cmClassFile.h
 cmMakeDepend.o : cmMakeDepend.h cmMakeDepend.cxx  cmMakefile.h cmClassFile.h cmRegularExpression.h
 cmRegularExpression.o : cmRegularExpression.h cmRegularExpression.cxx
diff --git a/Source/cmClassFile.cxx b/Source/cmClassFile.cxx
index f953bbb..6c219ed 100644
--- a/Source/cmClassFile.cxx
+++ b/Source/cmClassFile.cxx
@@ -2,23 +2,10 @@
 #pragma warning ( disable : 4786 )
 #endif
 #include "cmClassFile.h"
-#include <sys/stat.h>
+#include "cmSystemTools.h"
 #include <iostream>
 
 
-// Helper function to hide the use of system stat function
-bool cmFileExists(const char* filename)
-{
-  struct stat fs;
-  if (stat(filename, &fs) != 0) 
-  {
-    return false;
-  }
-  else
-  {
-    return true;
-  }
-}
 
 // Set the name of the class and the full path to the file.
 // The class must be found in dir and end in name.cxx, name.txx, 
@@ -37,7 +24,7 @@ void cmClassFile::SetName(const char* name, const char* dir)
   pathname += m_ClassName;
   std::string hname = pathname;
   hname += ".cxx";
-  if(cmFileExists(hname.c_str()))
+  if(cmSystemTools::FileExists(hname.c_str()))
     {
     m_HeaderFileOnly = false;
     m_FullPath = hname;
@@ -46,7 +33,7 @@ void cmClassFile::SetName(const char* name, const char* dir)
   
   hname = pathname;
   hname += ".c";
-  if(cmFileExists(hname.c_str()))
+  if(cmSystemTools::FileExists(hname.c_str()))
   {
     m_HeaderFileOnly = false;
     m_FullPath = hname;
@@ -54,13 +41,19 @@ void cmClassFile::SetName(const char* name, const char* dir)
   }
   hname = pathname;
   hname += ".txx";
-  if(cmFileExists(hname.c_str()))
+  if(cmSystemTools::FileExists(hname.c_str()))
   {
     m_HeaderFileOnly = false;
     m_FullPath = hname;
     return;
   }
-  std::cerr << "file seems to be a header only " << hname << " " << m_ClassName.c_str() << std::endl;
+  hname = pathname;
+  hname += ".h";
+  if(!cmSystemTools::FileExists(hname.c_str()))
+    {
+    std::cerr << "ERROR, can not find file " << hname;
+    std::cerr << "Tried .txx .cxx .c " << std::endl;
+    }
 }
 
 
diff --git a/Source/cmClassFile.h b/Source/cmClassFile.h
index f9e2f40..a8ad7b3 100644
--- a/Source/cmClassFile.h
+++ b/Source/cmClassFile.h
@@ -22,19 +22,25 @@
 #include <string>
 #include <vector>
 
-// helper function returns true if a file exits
-bool cmFileExists(const char* filename);
 
 struct cmClassFile
 {
-  // Set the name of the file
+  /**
+   * Set the name of the file, given the directory
+   * the file should be in.   Extensions are tried on 
+   * the name in the directory to find the actual file.
+   */
   void SetName(const char* name, const char* dir);
+  /**
+   * print the structure to cout
+   */
   void Print();
 
-  bool m_AbstractClass;
-  bool m_HeaderFileOnly;
-  std::string m_FullPath;
-  std::string m_ClassName;
+  bool m_AbstractClass;         // is this an abstract class
+  bool m_HeaderFileOnly;        // is this file only a header file
+  std::string m_FullPath;       // full path to the file
+  std::string m_ClassName;      // class name
+  // list of files that this file depends on
   std::vector<std::string> m_Depends;
 };
 
diff --git a/Source/cmDSPBuilder.cxx b/Source/cmDSPBuilder.cxx
deleted file mode 100644
index b732d96..0000000
--- a/Source/cmDSPBuilder.cxx
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifdef _MSC_VER
-#pragma warning ( disable : 4786 )
-#endif
-#include "cmDSPBuilder.h"
-#include "cmDSPMakefile.h"
-
-cmDSPBuilder::~cmDSPBuilder()
-{
-  delete m_Makefile;
-}
-
-cmDSPBuilder::cmDSPBuilder()
-{
-  m_Makefile = new cmDSPMakefile;
-}
-
-cmMakefile* cmDSPBuilder::GetMakefile()
-{
-  return m_Makefile;
-}
-
-
-void cmDSPBuilder::CreateDSPFile()
-{
-  m_Makefile->OutputDSPFile();
-}
-
-std::vector<std::string> cmDSPBuilder::GetCreatedProjectNames()
-{
-  return m_Makefile->GetCreatedProjectNames();
-}
diff --git a/Source/cmDSPBuilder.h b/Source/cmDSPBuilder.h
deleted file mode 100644
index 94d314b..0000000
--- a/Source/cmDSPBuilder.h
+++ /dev/null
@@ -1,40 +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.
-
-=========================================================================*/
-/**
- * cmDSPBuilder is a Facade class for cmDSWMakefile 
- */
-
-#ifndef __cmDSPBuilder_h
-#define __cmDSPBuilder_h
-#include "cmPCBuilder.h"
-#include <vector>
-#include <string>
-class cmDSPMakefile;
-
-class cmDSPBuilder : public cmPCBuilder
-{
-public:
-  cmDSPBuilder();
-  ~cmDSPBuilder();
-  void CreateDSPFile();
-  std::vector<std::string> GetCreatedProjectNames();  
-  virtual cmMakefile* GetMakefile();
-protected:
-  cmDSPMakefile* m_Makefile;
-};
-
-#endif
-
diff --git a/Source/cmDSPMakefile.cxx b/Source/cmDSPMakefile.cxx
index f140f5e..34625cd 100644
--- a/Source/cmDSPMakefile.cxx
+++ b/Source/cmDSPMakefile.cxx
@@ -1,8 +1,11 @@
 #include "cmDSPMakefile.h"
 #include "cmSystemTools.h"
+#include "cmCollectFlags.h"
 #include <iostream>
 #include <fstream>
+#define WIN32_LEAN_AND_MEAN
 #include <windows.h>
+#undef GetCurrentDirectory
 
 static void Die(const char* message)
 {
@@ -13,28 +16,49 @@ static void Die(const char* message)
 
 void cmDSPMakefile::OutputDSPFile()
 { 
-  m_IncludeOptions = "/STACK:10000000 ";
-  m_IncludeOptions = "/I \"";
-  m_IncludeOptions += this->GetHomeDirectory();
-  m_IncludeOptions += "/Code/Common\" ";
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetHomeDirectory();
-  m_IncludeOptions += "/Code/Insight3DParty/vxl\" ";
-  // Add the Build directory vcl to the -I path for config.h type stuff
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetOutputHomeDirectory();
-  m_IncludeOptions += "/Code/Insight3DParty/vxl\" ";
-  // Add the Build directory to the -I path for config.h type stuff
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetOutputHomeDirectory();
-  m_IncludeOptions += "\" ";
-  m_DebugLibraryOptions = " ITKCommon.lib ITKNumerics.lib ";
-  m_DebugLibraryOptions += " /LIBPATH:\"";
-  m_DebugLibraryOptions += this->GetOutputHomeDirectory();
-  m_DebugLibraryOptions += "/Code/Common/Debug\" ";
-  m_DebugLibraryOptions += " /LIBPATH:\"";
-  m_DebugLibraryOptions += this->GetOutputHomeDirectory();
-  m_DebugLibraryOptions += "/Code/Insight3DParty/vxl/Debug\" ";
+  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, "${CMAKE_CONFIG_DIR}",
+				 this->GetOutputHomeDirectory() );
+    cmSystemTools::ReplaceString(include, "${srcdir}",
+				 this->GetHomeDirectory() );
+    m_IncludeOptions +=  "/I \"";
+    m_IncludeOptions += include;
+    m_IncludeOptions += "\" ";
+    }
+  std::vector<std::string>& libs = m_BuildFlags.GetLinkLibraries();
+  for(i = libs.begin(); i != libs.end(); ++i)
+    {
+    m_DebugLibraryOptions += " ";
+    m_DebugLibraryOptions += *i;
+    m_DebugLibraryOptions += ".lib ";
+    }
+  std::vector<std::string>& libswin32 = m_BuildFlags.GetLinkLibrariesWin32();
+  for(i = libswin32.begin(); i != libswin32.end(); ++i)
+    {
+    m_DebugLibraryOptions += " ";
+    m_DebugLibraryOptions += *i;
+    m_DebugLibraryOptions += ".lib ";
+    }
+  std::vector<std::string>& libdirs = m_BuildFlags.GetLinkDirectories();
+  for(i = libdirs.begin(); i != libdirs.end(); ++i)
+    {
+    m_DebugLibraryOptions += " /LIBPATH:\"";
+    m_DebugLibraryOptions += *i;
+    cmSystemTools::ReplaceString(m_DebugLibraryOptions, "${CMAKE_CONFIG_DIR}",
+				 this->GetOutputHomeDirectory() );
+    if(i->find("Debug") == std::string::npos)
+      {
+      if(i->find("Release") == std::string::npos)
+	{
+	m_DebugLibraryOptions += "/Debug\" ";
+	}
+      }
+    }
+  m_DebugLibraryOptions += "/STACK:10000000 ";
   m_ReleaseLibraryOptions = m_DebugLibraryOptions;
   cmSystemTools::ReplaceString(m_ReleaseLibraryOptions, "Debug", "Release");
   // If the output directory is not the m_cmHomeDirectory
@@ -123,7 +147,6 @@ void cmDSPMakefile::WriteDSPBuildRule(std::ostream& fout)
 {
   std::string dspname = *(m_CreatedProjectNames.end()-1);
   dspname += ".dsp";
-#undef GetCurrentDirectory
   std::string makefileIn = this->GetCurrentDirectory();
   makefileIn += "/";
   makefileIn += "CMakeLists.txt";
diff --git a/Source/cmDSPWriter.cxx b/Source/cmDSPWriter.cxx
index f140f5e..34625cd 100644
--- a/Source/cmDSPWriter.cxx
+++ b/Source/cmDSPWriter.cxx
@@ -1,8 +1,11 @@
 #include "cmDSPMakefile.h"
 #include "cmSystemTools.h"
+#include "cmCollectFlags.h"
 #include <iostream>
 #include <fstream>
+#define WIN32_LEAN_AND_MEAN
 #include <windows.h>
+#undef GetCurrentDirectory
 
 static void Die(const char* message)
 {
@@ -13,28 +16,49 @@ static void Die(const char* message)
 
 void cmDSPMakefile::OutputDSPFile()
 { 
-  m_IncludeOptions = "/STACK:10000000 ";
-  m_IncludeOptions = "/I \"";
-  m_IncludeOptions += this->GetHomeDirectory();
-  m_IncludeOptions += "/Code/Common\" ";
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetHomeDirectory();
-  m_IncludeOptions += "/Code/Insight3DParty/vxl\" ";
-  // Add the Build directory vcl to the -I path for config.h type stuff
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetOutputHomeDirectory();
-  m_IncludeOptions += "/Code/Insight3DParty/vxl\" ";
-  // Add the Build directory to the -I path for config.h type stuff
-  m_IncludeOptions += "/I \"";
-  m_IncludeOptions += this->GetOutputHomeDirectory();
-  m_IncludeOptions += "\" ";
-  m_DebugLibraryOptions = " ITKCommon.lib ITKNumerics.lib ";
-  m_DebugLibraryOptions += " /LIBPATH:\"";
-  m_DebugLibraryOptions += this->GetOutputHomeDirectory();
-  m_DebugLibraryOptions += "/Code/Common/Debug\" ";
-  m_DebugLibraryOptions += " /LIBPATH:\"";
-  m_DebugLibraryOptions += this->GetOutputHomeDirectory();
-  m_DebugLibraryOptions += "/Code/Insight3DParty/vxl/Debug\" ";
+  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, "${CMAKE_CONFIG_DIR}",
+				 this->GetOutputHomeDirectory() );
+    cmSystemTools::ReplaceString(include, "${srcdir}",
+				 this->GetHomeDirectory() );
+    m_IncludeOptions +=  "/I \"";
+    m_IncludeOptions += include;
+    m_IncludeOptions += "\" ";
+    }
+  std::vector<std::string>& libs = m_BuildFlags.GetLinkLibraries();
+  for(i = libs.begin(); i != libs.end(); ++i)
+    {
+    m_DebugLibraryOptions += " ";
+    m_DebugLibraryOptions += *i;
+    m_DebugLibraryOptions += ".lib ";
+    }
+  std::vector<std::string>& libswin32 = m_BuildFlags.GetLinkLibrariesWin32();
+  for(i = libswin32.begin(); i != libswin32.end(); ++i)
+    {
+    m_DebugLibraryOptions += " ";
+    m_DebugLibraryOptions += *i;
+    m_DebugLibraryOptions += ".lib ";
+    }
+  std::vector<std::string>& libdirs = m_BuildFlags.GetLinkDirectories();
+  for(i = libdirs.begin(); i != libdirs.end(); ++i)
+    {
+    m_DebugLibraryOptions += " /LIBPATH:\"";
+    m_DebugLibraryOptions += *i;
+    cmSystemTools::ReplaceString(m_DebugLibraryOptions, "${CMAKE_CONFIG_DIR}",
+				 this->GetOutputHomeDirectory() );
+    if(i->find("Debug") == std::string::npos)
+      {
+      if(i->find("Release") == std::string::npos)
+	{
+	m_DebugLibraryOptions += "/Debug\" ";
+	}
+      }
+    }
+  m_DebugLibraryOptions += "/STACK:10000000 ";
   m_ReleaseLibraryOptions = m_DebugLibraryOptions;
   cmSystemTools::ReplaceString(m_ReleaseLibraryOptions, "Debug", "Release");
   // If the output directory is not the m_cmHomeDirectory
@@ -123,7 +147,6 @@ void cmDSPMakefile::WriteDSPBuildRule(std::ostream& fout)
 {
   std::string dspname = *(m_CreatedProjectNames.end()-1);
   dspname += ".dsp";
-#undef GetCurrentDirectory
   std::string makefileIn = this->GetCurrentDirectory();
   makefileIn += "/";
   makefileIn += "CMakeLists.txt";
diff --git a/Source/cmDSWBuilder.cxx b/Source/cmDSWBuilder.cxx
deleted file mode 100644
index d64db89..0000000
--- a/Source/cmDSWBuilder.cxx
+++ /dev/null
@@ -1,22 +0,0 @@
-#include "cmDSWBuilder.h"
-#include "cmDSWMakefile.h"
-
-cmDSWBuilder::~cmDSWBuilder()
-{
-  delete m_Makefile;
-}
-
-cmDSWBuilder::cmDSWBuilder()
-{
-  m_Makefile = new cmDSWMakefile;
-}
-
-cmMakefile* cmDSWBuilder::GetMakefile()
-{
-  return m_Makefile;
-}
-
-void cmDSWBuilder::CreateDSWFile()
-{
-  m_Makefile->OutputDSWFile();
-}
diff --git a/Source/cmDSWBuilder.h b/Source/cmDSWBuilder.h
deleted file mode 100644
index f44a01e..0000000
--- a/Source/cmDSWBuilder.h
+++ /dev/null
@@ -1,38 +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.
-
-=========================================================================*/
-/**
- * cmDSWBuilder 
- */
-
-#ifndef __cmDSWBuilder_h
-#define __cmDSWBuilder_h
-
-#include "cmPCBuilder.h"
-class cmDSWMakefile;
-
-class cmDSWBuilder : public cmPCBuilder
-{
-public:
-  cmDSWBuilder();
-  ~cmDSWBuilder();
-  void CreateDSWFile();
-  virtual cmMakefile* GetMakefile();
-protected:
-  cmDSWMakefile* m_Makefile;
-};
-
-#endif
-
diff --git a/Source/cmDSWMakefile.cxx b/Source/cmDSWMakefile.cxx
index 60d09f5..271bd3e 100644
--- a/Source/cmDSWMakefile.cxx
+++ b/Source/cmDSWMakefile.cxx
@@ -2,12 +2,15 @@
 #pragma warning ( disable : 4786 )
 #endif
 #include "cmDSWMakefile.h"
-#include "cmDSPBuilder.h"
 #include "cmSystemTools.h"
+#include "cmDSPMakefile.h"
 #include <iostream>
 #include <fstream>
 #include <windows.h>
 
+// microsoft nonsense
+#undef GetCurrentDirectory
+#undef SetCurrentDirectory
 
 // virtual override, ouput the makefile 
 void cmDSWMakefile::OutputDSWFile()
@@ -27,80 +30,139 @@ void cmDSWMakefile::OutputDSWFile()
       MessageBox(0, m_OutputDirectory.c_str(), 0, MB_OK);
       }
     }
-  
-  
   std::string fname;
   fname = m_OutputDirectory;
   fname += "/";
   fname += this->m_LibraryName;
   fname += ".dsw";
   std::cerr << "writting dsw file " << fname.c_str() << std::endl;
-
   std::ofstream fout(fname.c_str());
   if(!fout)
     {
-    std::cerr  << "Error can not open " << fname.c_str() << " for write" << std::endl;
+    std::cerr  << "Error can not open " 
+	       << fname.c_str() << " for write" << std::endl;
     return;
     }
   this->WriteDSWFile(fout);
 }
 
+// ------------------------------------------------
+// Recursive function to find all the CMakeLists.txt files
+// in a project.  As each file is read in, any directories in
+// the SUBDIR variable are also passed back to this function.
+// The result is a vector of cmDSPMakefile objects, one for
+// each directory with a CMakeLists.txt file
+//
+void cmDSWMakefile::FindAllCMakeListsFiles(const char* subdir,
+					   std::vector<cmDSPMakefile*>& makefiles)
+{
+  std::string currentDir = this->GetCurrentDirectory();
+  currentDir += "/";
+  currentDir += subdir;
+  currentDir += "/";
+  currentDir += "CMakeLists.txt";
+  // CMakeLists.txt exits in the subdirectory
+  // then create a cmDSPMakefile for it
+  if(cmSystemTools::FileExists(currentDir.c_str()))
+    {
+    // Create a new cmDSPMakefile to read the currentDir CMakeLists.txt file
+    cmDSPMakefile* dsp = new cmDSPMakefile;
+    // add it to the vector
+    makefiles.push_back(dsp);
+    // Set up the file with the current context
+    dsp->SetOutputHomeDirectory(this->GetOutputDirectory());
+    dsp->SetHomeDirectory(this->GetHomeDirectory());
+    // set the current directory in the Source as a full
+    // path
+    std::string currentDir = this->GetCurrentDirectory();
+    currentDir += "/";
+    currentDir += subdir;
+    dsp->SetCurrentDirectory(currentDir.c_str());
+    // Parse the CMakeLists.txt file
+    currentDir += "/CMakeLists.txt";
+    dsp->ReadMakefile(currentDir.c_str());
+    // Set the output directory which may be different than the source
+    std::string outdir = m_OutputDirectory;
+    outdir += "/";
+    outdir += subdir;
+    dsp->SetOutputDirectory(outdir.c_str());
+    // Create the DSP file
+    dsp->OutputDSPFile();
+    // Look at any sub directories parsed (SUBDIRS) and 
+    // recurse into them    
+    const std::vector<std::string>& subdirs = dsp->GetSubDirectories();
+    for(std::vector<std::string>::const_iterator i = subdirs.begin();
+	i != subdirs.end(); ++i)
+      {
+      // append the subdirectory to the current directoy subdir
+      std::string nextDir = subdir;
+      nextDir += "/";
+      nextDir += i->c_str();
+      // recurse into nextDir
+      this->FindAllCMakeListsFiles(nextDir.c_str(),
+				   makefiles);
+      }
+    }
+  else
+    {
+    std::cerr << "Can not find CMakeLists.txt in " << currentDir.c_str() 
+	      << std::endl;
+    }
+}
 
+
+// Write a DSW file to the stream
 void cmDSWMakefile::WriteDSWFile(std::ostream& fout)
 {
+  // Write out the header for a DSW file
   this->WriteDSWHeader(fout);
-  for(std::vector<std::string>::iterator i = m_SubDirectories.begin();
-      i != m_SubDirectories.end(); ++i)
+  // Create an array of dsp files for the project
+  std::vector<cmDSPMakefile*> dspfiles;
+  // loop over all the subdirectories for the DSW file,
+  // and find all sub directory projects
+  for(std::vector<std::string>::iterator j = m_SubDirectories.begin();
+      j != m_SubDirectories.end(); ++j)
     {
-    const char* dir = (*i).c_str();
-    std::vector<std::string> dspnames = this->CreateDSPFile(dir);
-    std::cerr << "Create dsp for " << dspnames.size() << " number of dsp files in " << dir << std::endl;
+    this->FindAllCMakeListsFiles(j->c_str(), dspfiles);
+    }
+  // For each DSP file created insert them into the DSW file
+  for(std::vector<cmDSPMakefile*>::iterator k = dspfiles.begin();
+      k != dspfiles.end(); ++k)
+    {
+    // Get the directory for the dsp file, it comes
+    // from the source, so it has the source path which needs
+    // to be removed as this may be built in a different directory
+    // than the source
+    std::string dir = (*k)->GetCurrentDirectory();
+    // Get the home directory with the trailing slash
+    std::string homedir = this->GetHomeDirectory();
+    homedir += "/";
+    // make the directory relative by removing the home directory part
+    cmSystemTools::ReplaceString(dir, homedir.c_str(), "");
+    // Get the list of create dsp files from the cmDSPMakefile, more
+    // than one dsp could have been created per input CMakeLists.txt file
+    std::vector<std::string> dspnames = (*k)->GetCreatedProjectNames();
+    std::cerr << "Create dsp for " 
+	      << dspnames.size()
+	      << " number of dsp files in " << dir << std::endl;
     for(std::vector<std::string>::iterator si = dspnames.begin();
 	si != dspnames.end(); ++si)
       {
-      std::string dspname = *si;
-      std::cerr << "Create dsp for " << (*si).c_str() << std::endl;
-      if(dspname == "")
-	{
-	std::cerr << "Project name not found in " << dir << "/CMakeLists.txt" << std::endl;
-	std::cerr << "Skipping Project " << std::endl;
-	}
-      else
-	{
-	std::string subdir = "./";
-	subdir += dir;
-	this->WriteProject(fout, dspname.c_str(), subdir.c_str());
-	}
+      // Write the project into the DSW file
+      this->WriteProject(fout, si->c_str(), dir.c_str());
       }
+    // delete the cmDSPMakefile object once done with it to avoid
+    // leaks
+    delete *k;
     }
+  // Write the footer for the DSW file
   this->WriteDSWFooter(fout);
 }
 
-std::vector<std::string> cmDSWMakefile::CreateDSPFile(const char* subdir)
-{
-#undef GetCurrentDirectory
-  std::string currentDir = this->GetCurrentDirectory();
-  currentDir += "/";
-  currentDir += subdir;
-  cmDSPBuilder dsp;
-  dsp.SetOutputHomeDirectory(this->GetOutputDirectory());
-  dsp.SetHomeDirectory(this->GetHomeDirectory());
-  dsp.SetMakefileDirectory(currentDir.c_str());
-  std::string outdir = m_OutputDirectory;
-  outdir += "/";
-  outdir += subdir;
-  dsp.SetOutputDirectory(outdir.c_str());
-  currentDir += "/";
-  currentDir += "CMakeLists.txt";
-  dsp.SetInputMakefilePath(currentDir.c_str());
-  dsp.CreateDSPFile();
-  return dsp.GetCreatedProjectNames();
-}
-
 
 void cmDSWMakefile::WriteProject(std::ostream& fout, 
-				  const char* dspname,
-				  const char* dir)
+				 const char* dspname,
+				 const char* dir)
 {
   fout << "###############################################################################\n\n";
   fout << "Project: \"" << dspname << "\"=" 
diff --git a/Source/cmDSWMakefile.h b/Source/cmDSWMakefile.h
index e4036a1..6c3fc9e 100644
--- a/Source/cmDSWMakefile.h
+++ b/Source/cmDSWMakefile.h
@@ -24,6 +24,7 @@
 
 #include "cmMakefile.h"
 #include <vector>
+class cmDSPMakefile;
 
 
 class cmDSWMakefile : public cmMakefile
@@ -31,9 +32,10 @@ class cmDSWMakefile : public cmMakefile
 public:
   virtual void OutputDSWFile();
 private:
+  void FindAllCMakeListsFiles(const char* subdir,
+			      std::vector<cmDSPMakefile*>&);
   void WriteDSWFile(std::ostream& fout);
   void WriteDSWHeader(std::ostream& fout);
-  std::vector<std::string> CreateDSPFile(const char* dir);
   void WriteProject(std::ostream& fout, 
 		     const char* name, const char* path);
   void WriteDSWFooter(std::ostream& fout);
diff --git a/Source/cmDSWWriter.cxx b/Source/cmDSWWriter.cxx
index 60d09f5..271bd3e 100644
--- a/Source/cmDSWWriter.cxx
+++ b/Source/cmDSWWriter.cxx
@@ -2,12 +2,15 @@
 #pragma warning ( disable : 4786 )
 #endif
 #include "cmDSWMakefile.h"
-#include "cmDSPBuilder.h"
 #include "cmSystemTools.h"
+#include "cmDSPMakefile.h"
 #include <iostream>
 #include <fstream>
 #include <windows.h>
 
+// microsoft nonsense
+#undef GetCurrentDirectory
+#undef SetCurrentDirectory
 
 // virtual override, ouput the makefile 
 void cmDSWMakefile::OutputDSWFile()
@@ -27,80 +30,139 @@ void cmDSWMakefile::OutputDSWFile()
       MessageBox(0, m_OutputDirectory.c_str(), 0, MB_OK);
       }
     }
-  
-  
   std::string fname;
   fname = m_OutputDirectory;
   fname += "/";
   fname += this->m_LibraryName;
   fname += ".dsw";
   std::cerr << "writting dsw file " << fname.c_str() << std::endl;
-
   std::ofstream fout(fname.c_str());
   if(!fout)
     {
-    std::cerr  << "Error can not open " << fname.c_str() << " for write" << std::endl;
+    std::cerr  << "Error can not open " 
+	       << fname.c_str() << " for write" << std::endl;
     return;
     }
   this->WriteDSWFile(fout);
 }
 
+// ------------------------------------------------
+// Recursive function to find all the CMakeLists.txt files
+// in a project.  As each file is read in, any directories in
+// the SUBDIR variable are also passed back to this function.
+// The result is a vector of cmDSPMakefile objects, one for
+// each directory with a CMakeLists.txt file
+//
+void cmDSWMakefile::FindAllCMakeListsFiles(const char* subdir,
+					   std::vector<cmDSPMakefile*>& makefiles)
+{
+  std::string currentDir = this->GetCurrentDirectory();
+  currentDir += "/";
+  currentDir += subdir;
+  currentDir += "/";
+  currentDir += "CMakeLists.txt";
+  // CMakeLists.txt exits in the subdirectory
+  // then create a cmDSPMakefile for it
+  if(cmSystemTools::FileExists(currentDir.c_str()))
+    {
+    // Create a new cmDSPMakefile to read the currentDir CMakeLists.txt file
+    cmDSPMakefile* dsp = new cmDSPMakefile;
+    // add it to the vector
+    makefiles.push_back(dsp);
+    // Set up the file with the current context
+    dsp->SetOutputHomeDirectory(this->GetOutputDirectory());
+    dsp->SetHomeDirectory(this->GetHomeDirectory());
+    // set the current directory in the Source as a full
+    // path
+    std::string currentDir = this->GetCurrentDirectory();
+    currentDir += "/";
+    currentDir += subdir;
+    dsp->SetCurrentDirectory(currentDir.c_str());
+    // Parse the CMakeLists.txt file
+    currentDir += "/CMakeLists.txt";
+    dsp->ReadMakefile(currentDir.c_str());
+    // Set the output directory which may be different than the source
+    std::string outdir = m_OutputDirectory;
+    outdir += "/";
+    outdir += subdir;
+    dsp->SetOutputDirectory(outdir.c_str());
+    // Create the DSP file
+    dsp->OutputDSPFile();
+    // Look at any sub directories parsed (SUBDIRS) and 
+    // recurse into them    
+    const std::vector<std::string>& subdirs = dsp->GetSubDirectories();
+    for(std::vector<std::string>::const_iterator i = subdirs.begin();
+	i != subdirs.end(); ++i)
+      {
+      // append the subdirectory to the current directoy subdir
+      std::string nextDir = subdir;
+      nextDir += "/";
+      nextDir += i->c_str();
+      // recurse into nextDir
+      this->FindAllCMakeListsFiles(nextDir.c_str(),
+				   makefiles);
+      }
+    }
+  else
+    {
+    std::cerr << "Can not find CMakeLists.txt in " << currentDir.c_str() 
+	      << std::endl;
+    }
+}
 
+
+// Write a DSW file to the stream
 void cmDSWMakefile::WriteDSWFile(std::ostream& fout)
 {
+  // Write out the header for a DSW file
   this->WriteDSWHeader(fout);
-  for(std::vector<std::string>::iterator i = m_SubDirectories.begin();
-      i != m_SubDirectories.end(); ++i)
+  // Create an array of dsp files for the project
+  std::vector<cmDSPMakefile*> dspfiles;
+  // loop over all the subdirectories for the DSW file,
+  // and find all sub directory projects
+  for(std::vector<std::string>::iterator j = m_SubDirectories.begin();
+      j != m_SubDirectories.end(); ++j)
     {
-    const char* dir = (*i).c_str();
-    std::vector<std::string> dspnames = this->CreateDSPFile(dir);
-    std::cerr << "Create dsp for " << dspnames.size() << " number of dsp files in " << dir << std::endl;
+    this->FindAllCMakeListsFiles(j->c_str(), dspfiles);
+    }
+  // For each DSP file created insert them into the DSW file
+  for(std::vector<cmDSPMakefile*>::iterator k = dspfiles.begin();
+      k != dspfiles.end(); ++k)
+    {
+    // Get the directory for the dsp file, it comes
+    // from the source, so it has the source path which needs
+    // to be removed as this may be built in a different directory
+    // than the source
+    std::string dir = (*k)->GetCurrentDirectory();
+    // Get the home directory with the trailing slash
+    std::string homedir = this->GetHomeDirectory();
+    homedir += "/";
+    // make the directory relative by removing the home directory part
+    cmSystemTools::ReplaceString(dir, homedir.c_str(), "");
+    // Get the list of create dsp files from the cmDSPMakefile, more
+    // than one dsp could have been created per input CMakeLists.txt file
+    std::vector<std::string> dspnames = (*k)->GetCreatedProjectNames();
+    std::cerr << "Create dsp for " 
+	      << dspnames.size()
+	      << " number of dsp files in " << dir << std::endl;
     for(std::vector<std::string>::iterator si = dspnames.begin();
 	si != dspnames.end(); ++si)
       {
-      std::string dspname = *si;
-      std::cerr << "Create dsp for " << (*si).c_str() << std::endl;
-      if(dspname == "")
-	{
-	std::cerr << "Project name not found in " << dir << "/CMakeLists.txt" << std::endl;
-	std::cerr << "Skipping Project " << std::endl;
-	}
-      else
-	{
-	std::string subdir = "./";
-	subdir += dir;
-	this->WriteProject(fout, dspname.c_str(), subdir.c_str());
-	}
+      // Write the project into the DSW file
+      this->WriteProject(fout, si->c_str(), dir.c_str());
       }
+    // delete the cmDSPMakefile object once done with it to avoid
+    // leaks
+    delete *k;
     }
+  // Write the footer for the DSW file
   this->WriteDSWFooter(fout);
 }
 
-std::vector<std::string> cmDSWMakefile::CreateDSPFile(const char* subdir)
-{
-#undef GetCurrentDirectory
-  std::string currentDir = this->GetCurrentDirectory();
-  currentDir += "/";
-  currentDir += subdir;
-  cmDSPBuilder dsp;
-  dsp.SetOutputHomeDirectory(this->GetOutputDirectory());
-  dsp.SetHomeDirectory(this->GetHomeDirectory());
-  dsp.SetMakefileDirectory(currentDir.c_str());
-  std::string outdir = m_OutputDirectory;
-  outdir += "/";
-  outdir += subdir;
-  dsp.SetOutputDirectory(outdir.c_str());
-  currentDir += "/";
-  currentDir += "CMakeLists.txt";
-  dsp.SetInputMakefilePath(currentDir.c_str());
-  dsp.CreateDSPFile();
-  return dsp.GetCreatedProjectNames();
-}
-
 
 void cmDSWMakefile::WriteProject(std::ostream& fout, 
-				  const char* dspname,
-				  const char* dir)
+				 const char* dspname,
+				 const char* dir)
 {
   fout << "###############################################################################\n\n";
   fout << "Project: \"" << dspname << "\"=" 
diff --git a/Source/cmDSWWriter.h b/Source/cmDSWWriter.h
index e4036a1..6c3fc9e 100644
--- a/Source/cmDSWWriter.h
+++ b/Source/cmDSWWriter.h
@@ -24,6 +24,7 @@
 
 #include "cmMakefile.h"
 #include <vector>
+class cmDSPMakefile;
 
 
 class cmDSWMakefile : public cmMakefile
@@ -31,9 +32,10 @@ class cmDSWMakefile : public cmMakefile
 public:
   virtual void OutputDSWFile();
 private:
+  void FindAllCMakeListsFiles(const char* subdir,
+			      std::vector<cmDSPMakefile*>&);
   void WriteDSWFile(std::ostream& fout);
   void WriteDSWHeader(std::ostream& fout);
-  std::vector<std::string> CreateDSPFile(const char* dir);
   void WriteProject(std::ostream& fout, 
 		     const char* name, const char* path);
   void WriteDSWFooter(std::ostream& fout);
diff --git a/Source/cmMakeDepend.cxx b/Source/cmMakeDepend.cxx
index 4738373..ea1e6b5 100644
--- a/Source/cmMakeDepend.cxx
+++ b/Source/cmMakeDepend.cxx
@@ -2,23 +2,27 @@
 #pragma warning ( disable : 4786 )
 #endif
 #include "cmMakeDepend.h"
+#include "cmSystemTools.h"
 #include <fstream>
 #include <iostream>
 #include <algorithm>
 #include <functional>
 
 
-void cmMakeDepend::SetIncludeRegularExpression(const char* prefix)
-{
-  m_IncludeFileRegularExpression.compile(prefix);
-}
-
 cmMakeDepend::cmMakeDepend()
 {
   m_Verbose = false;
   m_IncludeFileRegularExpression.compile("^itk|^vtk|^vnl|^vcl|^f2c");
 }
 
+
+// only files matching this regular expression with be considered
+void cmMakeDepend::SetIncludeRegularExpression(const char* prefix)
+{
+  m_IncludeFileRegularExpression.compile(prefix);
+}
+
+
 cmMakeDepend::~cmMakeDepend()
 { 
   for(DependArray::iterator i = m_DependInformation.begin();
@@ -32,11 +36,25 @@ cmMakeDepend::~cmMakeDepend()
 
 // Set the makefile that depends will be made from.
 // The pointer is kept so the cmClassFile array can
-// be updated with the depend information. 
+// be updated with the depend information in the cmMakefile.
 
 void cmMakeDepend::SetMakefile(cmMakefile* makefile)
 {
   m_Makefile = makefile;
+  
+  // Now extract any include paths from the makefile flags
+  cmCollectFlags& flags = m_Makefile->GetBuildFlags();
+  std::vector<std::string>& includes = flags.GetIncludeDirectories();
+  std::vector<std::string>::iterator j;
+  for(j = includes.begin(); j != includes.end(); ++j)
+    {
+    cmSystemTools::ReplaceString(*j, "${CMAKE_CONFIG_DIR}",
+				 m_Makefile->GetOutputHomeDirectory() );
+    cmSystemTools::ReplaceString(*j, "${srcdir}",
+				 m_Makefile->GetHomeDirectory() );
+    this->AddSearchPath(j->c_str());
+    }
+  // Now create cmDependInformation objects for files in the directory
   int index = 0;
   std::vector<cmClassFile>::iterator i = makefile->m_Classes.begin();
   while(i != makefile->m_Classes.end())
@@ -49,7 +67,6 @@ void cmMakeDepend::SetMakefile(cmMakefile* makefile)
       info->m_IncludeName = (*i).m_FullPath;
       m_DependInformation.push_back(info);
       info->m_ClassFileIndex = index;
-      
       }
     ++i;
     index++;
@@ -195,6 +212,9 @@ int cmMakeDepend::FindInformation(const char* fname)
     }
   cmDependInformation* newinfo = new cmDependInformation;
   newinfo->m_FullPath = this->FullPath(fname);
+  // Add the directory where this file was found to the search path
+  // may have been foo/bar.h, but bar may include files from the foo
+  // directory without the foo prefix
   this->AddFileToSearchPath(newinfo->m_FullPath.c_str());
   newinfo->m_IncludeName = fname;
   m_DependInformation.push_back(newinfo);
@@ -204,13 +224,15 @@ int cmMakeDepend::FindInformation(const char* fname)
 // remove duplicate indices from the depend information 
 void cmDependInformation::RemoveDuplicateIndices()
 {
+  // sort the array
   std::sort(m_Indices.begin(), m_Indices.end(), std::less<int>());
+  // remove duplicates
   std::vector<int>::iterator new_end = 
     std::unique(m_Indices.begin(), m_Indices.end());
   m_Indices.erase(new_end, m_Indices.end());
 }
 
-// add the depend information from info to this
+// add the depend information from info to the m_Indices varible of this class.
 void cmDependInformation::MergeInfo(cmDependInformation* info)
 {
   std::vector<int>::iterator i = info->m_Indices.begin();
@@ -226,19 +248,19 @@ std::string cmMakeDepend::FullPath(const char* fname)
   for(std::vector<std::string>::iterator i = m_IncludeDirectories.begin();
       i != m_IncludeDirectories.end(); ++i)
     {
-    if(cmFileExists(fname))
+    if(cmSystemTools::FileExists(fname))
       {
       return std::string(fname);
       }
     std::string path = *i;
     path = path + "/";
     path = path + fname;
-    if(cmFileExists(path.c_str()))
+    if(cmSystemTools::FileExists(path.c_str()))
       {
       return path;
       }
     }
-  std::cerr << "File not found " << fname  << std::endl;
+  std::cerr << "Depend: File not found " << fname  << std::endl;
   return std::string(fname);
 }
 
diff --git a/Source/cmMakefile.cxx b/Source/cmMakefile.cxx
index 38792a5..3fa59a9 100644
--- a/Source/cmMakefile.cxx
+++ b/Source/cmMakefile.cxx
@@ -4,39 +4,11 @@
 #include "cmMakefile.h"
 #include "cmClassFile.h"
 #include "cmDirectory.h"
-
+#include "cmSystemTools.h"
 #include <fstream>
 #include <iostream>
 
 
-// remove extra spaces and the "\" character from the name
-// of the class as it is in the CMakeLists.txt
-inline std::string CleanUpName(const char* name)
-{
-  std::string className = name;
-  size_t i =0;
-  while(className[i] == ' ')
-    {
-    i++;
-    }
-  if(i)
-    {
-    className = className.substr(i, className.size());
-    } 
-  size_t pos = className.find('\\');
-  if(pos != std::string::npos)
-    {
-    className = className.substr(0, pos);
-    }
-  
-  pos = className.find(' ');
-  if(pos != std::string::npos)
-    {
-    className = className.substr(0, pos);
-    }
-  return className;
-}
-
 // default is not to be building executables
 cmMakefile::cmMakefile()
 {
@@ -55,7 +27,10 @@ void cmMakefile::Print()
 
 bool cmMakefile::ReadMakefile(const char* filename)
 {
-  std::cerr << "reading makefile " << filename << std::endl;
+  m_BuildFlags.SetSourceHomeDirectory(this->GetHomeDirectory());
+  m_BuildFlags.SetStartDirectory(this->GetCurrentDirectory());
+  m_BuildFlags.ParseDirectories();
+
   std::ifstream fin(filename);
   if(!fin)
     {
@@ -106,7 +81,7 @@ bool cmMakefile::ReadMakefile(const char* filename)
       {
       if(line.find("\\") != std::string::npos)
 	{
-	this->ReadSubdirs(fin);
+        cmSystemTools::ReadList(m_SubDirectories, fin);
 	}
       }
     else if(line.find("EXECUTABLES") != std::string::npos)
@@ -177,7 +152,7 @@ void cmMakefile::ReadClasses(std::ifstream& fin,
       done = true;
       }
     // remove extra spaces and \ from the class name
-    classname = CleanUpName(classname.c_str());
+    classname = cmSystemTools::CleanUpName(classname.c_str());
     
     // if this is not an abstract list then add new class
     // to the list of classes in this makefile
@@ -204,6 +179,9 @@ void cmMakefile::ReadClasses(std::ifstream& fin,
     }
 }
 
+// Find all of the files in dir as specified from this line:
+// TEMPLATE_INSTANCE_DIRECTORY = dir
+// Add all the files to the m_Classes array.
 
 void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
 {
@@ -211,7 +189,7 @@ void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
   if(start != std::string::npos)
     {
     std::string dirname = line.substr(start+1, line.size());
-    dirname = CleanUpName(dirname.c_str());
+    dirname = cmSystemTools::CleanUpName(dirname.c_str());
     std::string tdir = this->GetCurrentDirectory();
     tdir += "/";
     tdir += dirname;
@@ -250,28 +228,3 @@ void cmMakefile::ReadTemplateInstanceDirectory(std::string& line)
 }
 
 
-
-// Read a list of subdirectories from the stream
-void cmMakefile::ReadSubdirs(std::ifstream& fin)
-{
-  char inbuffer[2048];
-  bool done = false;
-
-  while (!done)
-    {  
-    // read a line from the makefile
-    fin.getline(inbuffer, 2047); 
-    // convert to a string class
-    std::string dir = inbuffer;
-    // if the line does not end in \ then we are at the
-    // end of the list
-    if(dir.find('\\') == std::string::npos)
-      {
-      done = true;
-      }
-    // remove extra spaces and \ from the class name
-    dir = CleanUpName(dir.c_str());
-    m_SubDirectories.push_back(dir);
-    }
-}
-
diff --git a/Source/cmMakefile.h b/Source/cmMakefile.h
index d570de4..94cb988 100644
--- a/Source/cmMakefile.h
+++ b/Source/cmMakefile.h
@@ -14,7 +14,8 @@
 
 =========================================================================*/
 /**
- * cmMakefile
+ * cmMakefile - used to parse and store the contents of a
+ * CMakeLists.txt makefile in memory.
  */
 #ifndef cmMakefile_h
 #define cmMakefile_h
@@ -23,6 +24,7 @@
 #endif
 
 #include "cmClassFile.h"
+#include "cmCollectFlags.h"
 #include <vector>
 #include <fstream>
 #include <iostream>
@@ -82,10 +84,17 @@ public:
     {
       return m_OutputHomeDirectory.c_str();
     }
+  cmCollectFlags& GetBuildFlags() 
+    {
+      return m_BuildFlags;
+    }
+  const std::vector<std::string>& GetSubDirectories()
+    { 
+      return m_SubDirectories;
+    }
   
 private:
   void ReadTemplateInstanceDirectory(std::string&);
-  void ReadSubdirs(std::ifstream& fin);
   void ReadClasses(std::ifstream& fin, bool t);
   friend class cmMakeDepend;	// make depend needs direct access 
 				// to the m_Classes array
@@ -99,7 +108,8 @@ protected:
   std::string m_LibraryName;	// library name
   std::vector<cmClassFile> m_Classes; // list of classes in makefile
   std::vector<std::string> m_SubDirectories; // list of sub directories
-  std::vector<std::string> m_MakeVerbatim; // list of sub directories
+  std::vector<std::string> m_MakeVerbatim; // lines copied from input file
+  cmCollectFlags m_BuildFlags;
 };
 
 
diff --git a/Source/cmPCBuilder.cxx b/Source/cmPCBuilder.cxx
deleted file mode 100644
index e8745c5..0000000
--- a/Source/cmPCBuilder.cxx
+++ /dev/null
@@ -1,46 +0,0 @@
-#include "cmPCBuilder.h"
-#include "cmMakefile.h"
-
-
-cmPCBuilder::cmPCBuilder()
-{
-}
- 
-// Delete the m_Makefile
-cmPCBuilder::~cmPCBuilder()
-{
-}
-
-// Read in the given makefile
-void cmPCBuilder::SetInputMakefilePath(const char* mfile)
-{
-  if(!GetMakefile()->ReadMakefile(mfile))
-    {
-    std::cerr << "Error can not open " << mfile << " for input " << std::endl;
-    abort();
-    }
-}
-
-
-void cmPCBuilder::SetHomeDirectory(const char* dir)
-{
-  GetMakefile()->SetHomeDirectory(dir);
-} 
-
-void cmPCBuilder::SetMakefileDirectory(const char* dir)
-{
-  GetMakefile()->SetCurrentDirectory(dir);
-}
-
-
-
-void cmPCBuilder::SetOutputDirectory(const char* dir)
-{
-  GetMakefile()->SetOutputDirectory(dir);
-}
-
-void cmPCBuilder::SetOutputHomeDirectory(const char* dir)
-{
-  GetMakefile()->SetOutputHomeDirectory(dir);
-}
-
diff --git a/Source/cmPCBuilder.h b/Source/cmPCBuilder.h
deleted file mode 100644
index e541bfc..0000000
--- a/Source/cmPCBuilder.h
+++ /dev/null
@@ -1,43 +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.
-
-=========================================================================*/
-/**
- * cmPCBuilder 
- */
-
-#ifndef __cmPCBuilder_h
-#define __cmPCBuilder_h
-class cmMakefile;
-/**
- * cmPCBuilder is a supper class used for creating a build
- * file for PC's.  This class can parse an cm Makefile.in and
- * extract the classes that need to be compiled.
- */
-
-class cmPCBuilder 
-{
-public:
-  cmPCBuilder();
-  ~cmPCBuilder();
-  virtual cmMakefile* GetMakefile() = 0;
-  void SetInputMakefilePath(const char*);
-  void SetHomeDirectory(const char*);
-  void SetMakefileDirectory(const char*);
-  void SetOutputDirectory(const char*);
-  void SetOutputHomeDirectory(const char*);
-};
-
-#endif
-
diff --git a/Source/cmSystemTools.cxx b/Source/cmSystemTools.cxx
index 49dc32b..b8a44c9 100644
--- a/Source/cmSystemTools.cxx
+++ b/Source/cmSystemTools.cxx
@@ -1,7 +1,52 @@
 #include "cmSystemTools.h"
-#include <direct.h>
 #include "errno.h"
+#include <sys/stat.h>
+
+#ifdef _MSC_VER
 #include <windows.h>
+#include <direct.h>
+inline int Mkdir(const char* dir)
+{
+  return _mkdir(dir);
+}
+#else
+#include <sys/types.h>
+#include <fcntl.h>
+#include <unistd.h>
+inline int Mkdir(const char* dir)
+{
+  return mkdir(dir, 00700);
+}
+#endif
+
+// remove extra spaces and the "\" character from the name
+// of the class as it is in the CMakeLists.txt
+std::string cmSystemTools::CleanUpName(const char* name)
+{
+  std::string className = name;
+  size_t i =0;
+  while(className[i] == ' ')
+    {
+    i++;
+    }
+  if(i)
+    {
+    className = className.substr(i, className.size());
+    } 
+  size_t pos = className.find('\\');
+  if(pos != std::string::npos)
+    {
+    className = className.substr(0, pos);
+    }
+  
+  pos = className.find(' ');
+  if(pos != std::string::npos)
+    {
+    className = className.substr(0, pos);
+    }
+  return className;
+}
+
 
 bool cmSystemTools::MakeDirectory(const char* path)
 {
@@ -21,10 +66,10 @@ bool cmSystemTools::MakeDirectory(const char* path)
   while((pos = dir.find('/', pos)) != std::string::npos)
     {
     std::string topdir = dir.substr(0, pos);
-    _mkdir(topdir.c_str());
+    Mkdir(topdir.c_str());
     pos++;
     }
-  if(_mkdir(path) != 0)
+  if(Mkdir(path) != 0)
     {
     // if it is some other error besides directory exists
     // then return false
@@ -36,6 +81,9 @@ bool cmSystemTools::MakeDirectory(const char* path)
   return true;
 }
 
+
+// replace replace with with as many times as it shows up in source.
+// write the result into source.
 void cmSystemTools::ReplaceString(std::string& source,
                                    const char* replace,
                                    const char* with)
@@ -52,3 +100,57 @@ void cmSystemTools::ReplaceString(std::string& source,
     start = source.find(replace, start + lengthReplace );
     }
 }
+
+// return true if the file exists
+bool cmSystemTools::FileExists(const char* filename)
+{
+  struct stat fs;
+  if (stat(filename, &fs) != 0) 
+  {
+    return false;
+  }
+  else
+  {
+    return true;
+  }
+}
+
+// Read a list from a CMakeLists.txt file open stream.
+// assume the stream has just read "VAR = \"
+// read until there is not a "\" at the end of the line.
+void cmSystemTools::ReadList(std::vector<std::string>& stringList, 
+                             std::ifstream& fin)
+{
+  char inbuffer[2048];
+  bool done = false;
+  while ( !done )
+    {
+    fin.getline(inbuffer, 2047 );
+    std::string inname = inbuffer;
+    if(inname.find('\\') == std::string::npos)
+      {
+      done = true;
+      }
+    if(inname.size())
+      {
+      stringList.push_back(cmSystemTools::CleanUpName(inname.c_str()));
+      }
+    }
+}
+
+
+// convert windows slashes to unix slashes \ with /
+void cmSystemTools::ConvertToUnixSlashes(std::string& path)
+{
+  std::string::size_type pos = path.find('\\');
+  while(pos != std::string::npos)
+    {
+    path[pos] = '/';
+    pos = path.find('\\');
+    }
+  // remove any trailing slash
+  if(path[path.size()-1] == '/')
+    {
+    path = path.substr(0, path.size()-1);
+    }
+}
diff --git a/Source/cmSystemTools.h b/Source/cmSystemTools.h
index a7b00f7..d4745f4 100644
--- a/Source/cmSystemTools.h
+++ b/Source/cmSystemTools.h
@@ -14,23 +14,56 @@
 
 =========================================================================*/
 /**
- * cmWindowsTools
+ * cmSystemTools - a collection of useful functions for CMake.
  */
-#ifndef cmWindowsTools_h
-#define cmWindowsTools_h
+#ifndef cmSystemTools_h
+#define cmSystemTools_h
 #ifdef _MSC_VER
 #pragma warning ( disable : 4786 )
 #endif
 
 #include <string>
+#include <vector>
+#include <fstream>
 
 class cmSystemTools
 {
 public:
+  /**
+   * Make a new directory if it is not there.  This function
+   * can make a full path even if none of the directories existed
+   * prior to calling this function.  
+   */
   static bool MakeDirectory(const char* path);
+  /**
+   * Replace replace all occurances of the string in in
+   * souce string.
+   */
   static void ReplaceString(std::string& source,
                             const char* replace,
                             const char* with);
+  /**
+   *  Remove extra spaces and the trailing \ from a string.
+   */
+  static std::string CleanUpName(const char* name);
+  /**
+   * Replace windows slashes with unix style slashes
+   */
+  static void ConvertToUnixSlashes(std::string& path);
+ 
+  /**
+   * Return true if a file exists
+   */
+  static bool FileExists(const char* filename);
+  /**
+   * Read a list from a file into the array of strings.
+   * This function assumes that the first line of the
+   * list has been read.  For example: NAME = \ was already
+   * read in.   The reading stops when there are no more
+   * continuation characters.
+   */
+  static void ReadList(std::vector<std::string>& stringList, 
+                       std::ifstream& fin);
 };
 
 
diff --git a/Source/cmUnixMakefile.cxx b/Source/cmUnixMakefile.cxx
index 90c887b..83f215c 100644
--- a/Source/cmUnixMakefile.cxx
+++ b/Source/cmUnixMakefile.cxx
@@ -53,7 +53,14 @@ inline std::string FixDirectoryName(const char* dir)
   return s;
 }
 
-// output the makefile to the named file
+// This is where CMakeTargets.make is generated
+// This function ouputs the following:
+// 1. Include flags for the compiler
+// 2. List of .o files that need to be compiled
+// 3. Rules to build executables including -l and -L options
+// 4. Rules to build in sub directories
+// 5. The name of the library being built, if it is a library
+
 void cmUnixMakefile::OutputMakefile(const char* file)
 {
   std::ofstream fout(file);
@@ -62,8 +69,28 @@ void cmUnixMakefile::OutputMakefile(const char* file)
     std::cerr  << "Error can not open " << file << " for write" << std::endl;
     return;
     }
+  // Output Include paths
+  fout << "INCLUDE_FLAGS = ";
+  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;
+    fout << "-I" << i->c_str() << " ";
+    }
+  fout << " ${LOCAL_INCLUDE_FLAGS} ";
+  fout << "\n";
+  // see if there are files to compile in this makefile
+  // These are used for both libraries and executables
   if(m_Classes.size() )
     {
+    // Ouput Library name if there are SRC_OBJS
+    if(strlen(this->GetLibraryName()) > 0)
+      {
+      fout << "ME = " <<  this->GetLibraryName() << "\n\n";
+      fout << "BUILD_LIB_FILE = lib${ME}${ITK_LIB_EXT}\n\n";
+      }
+    // Output SRC_OBJ list for all the classes to be compiled
     fout << "SRC_OBJ = \\\n";
     for(int i = 0; i < m_Classes.size(); i++)
       {
@@ -82,20 +109,41 @@ void cmUnixMakefile::OutputMakefile(const char* file)
       }
     fout << "\n";
     }
-  if(strlen(this->GetLibraryName()) > 0)
-    {
-    fout << "ME = " <<  this->GetLibraryName() << "\n\n";
-    fout << "BUILD_LIB_FILE = lib${ME}${ITK_LIB_EXT}\n\n";
-    }
-
+  // Ouput user make text embeded in the input file
   for(int i =0; i < m_MakeVerbatim.size(); i++)
     {
     fout << m_MakeVerbatim[i] << "\n";
     }
   fout << "\n\n";
 
+  // Output rules for building executables  
   if( m_Executables )
     {
+    // collect all the flags needed for linking libraries
+    std::string linkLibs;        
+    std::vector<std::string>::iterator j;
+    std::vector<std::string>& libdirs = m_BuildFlags.GetLinkDirectories();
+    for(j = libdirs.begin(); j != libdirs.end(); ++j)
+      {
+      linkLibs += "-L";
+      linkLibs += *j;
+      linkLibs += " ";
+      }
+    std::vector<std::string>& libs = m_BuildFlags.GetLinkLibraries();
+    for(j = libs.begin(); j != libs.end(); ++j)
+      {
+      linkLibs += "-l";
+      linkLibs += *j;
+      linkLibs += " ";
+      }
+    std::vector<std::string>& libsUnix = m_BuildFlags.GetLinkLibrariesUnix();
+    for(j = libsUnix.begin(); j != libsUnix.end(); ++j)
+      {
+      linkLibs += *j;
+      linkLibs += " ";
+      }
+    linkLibs += " ${LOCAL_LINK_FLAGS} ";
+    // Now create rules for all of the executables to be built
     for(int i = 0; i < m_Classes.size(); i++)
       {
       if(!m_Classes[i].m_AbstractClass && !m_Classes[i].m_HeaderFileOnly)
@@ -103,10 +151,13 @@ void cmUnixMakefile::OutputMakefile(const char* file)
         std::string DotO = m_Classes[i].m_ClassName;
         DotO += ".o";
         fout << m_Classes[i].m_ClassName << ": " << DotO << "\n";
-	fout << "\t ${CXX}  ${CXX_FLAGS}  " << DotO.c_str() << " -o $@ -L${CMAKE_OBJ_DIR}/Code/Common -lITKCommon \\\n"
-	     << "\t-L${CMAKE_OBJ_DIR}/Code/Insight3DParty/vxl -lITKNumerics -lm ${DL_LIBS}\n\n";
+	fout << "\t${CXX}  ${CXX_FLAGS}  " 
+	     << DotO.c_str() << " "
+             << linkLibs.c_str() 
+	     << " -o $@ ""\n\n";
 	}
       }
+    // ouput the list of executables
     fout << "EXECUTABLES = \\\n";
     for(int i = 0; i < m_Classes.size(); i++)
       {
@@ -122,7 +173,7 @@ void cmUnixMakefile::OutputMakefile(const char* file)
       }
     fout << "\n";
     }
-  
+  // Output Sub directory build rules
   if( m_SubDirectories.size() )
     {
     fout << "SUBDIR_BUILD = \\\n";
diff --git a/Source/cmUnixMakefile.h b/Source/cmUnixMakefile.h
index 67c0911..220a07d 100644
--- a/Source/cmUnixMakefile.h
+++ b/Source/cmUnixMakefile.h
@@ -25,7 +25,9 @@
 class cmUnixMakefile : public cmMakefile
 {
 public:
-  // Write the makefile to the named file
+  /** 
+   * Write the makefile to the named file
+   */
   void OutputMakefile(const char* file);
 protected:
   void OutputDepends(std::ostream&);
diff --git a/Source/cmWindowsConfigure.h b/Source/cmWindowsConfigure.h
index 662e07d..e0a7413 100644
--- a/Source/cmWindowsConfigure.h
+++ b/Source/cmWindowsConfigure.h
@@ -26,10 +26,16 @@
 class cmWindowsConfigure
 {
 public:
+  /**
+   * Set the path to the top level of the source directory
+   */
   void SetWhereSource(const char* dir) 
     {
       m_WhereSource = dir;
     }
+  /**
+   * Set the path to the top level of the build directory
+   */
   void SetWhereBuild(const char* dir)
     {
       m_WhereBuild = dir;
diff --git a/Source/itkVC60Configure.h b/Source/itkVC60Configure.h
index b86b0ea..a30c71e 100644
--- a/Source/itkVC60Configure.h
+++ b/Source/itkVC60Configure.h
@@ -25,8 +25,17 @@
 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,