ENH:Documentation and cleanups

24 files changed, 862 insertions, 383 deletions

diff --git a/Source/CMakeSetupCMD.cxx b/Source/CMakeSetupCMD.cxx
index fabae5a..90c4e30 100644
--- a/Source/CMakeSetupCMD.cxx
+++ b/Source/CMakeSetupCMD.cxx
@@ -54,11 +54,11 @@ int main(int ac, char** av)
   cmMSProjectGenerator* pg = new cmMSProjectGenerator;
   if(arg.find("-DSP", 0) != std::string::npos)
     {
-    pg->SetBuildDSP();
+    pg->BuildDSPOff();
     }
   else
     {
-    pg->SetBuildDSW();
+    pg->BuildDSWOn();
     }
   builder.SetMakefileGenerator(pg);
   builder.ReadMakefile(av[1]);
diff --git a/Source/cmAddTargetRule.cxx b/Source/cmAddTargetRule.cxx
index ff1c728..c115e75 100644
--- a/Source/cmAddTargetRule.cxx
+++ b/Source/cmAddTargetRule.cxx
@@ -1,3 +1,18 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
 #include "cmAddTargetRule.h"
 
 // cmAddTargetRule
diff --git a/Source/cmAuxSourceDirectoryRule.cxx b/Source/cmAuxSourceDirectoryRule.cxx
index e7c5211..1b7f45a 100644
--- a/Source/cmAuxSourceDirectoryRule.cxx
+++ b/Source/cmAuxSourceDirectoryRule.cxx
@@ -1,3 +1,18 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
 #include "cmAuxSourceDirectoryRule.h"
 #include "cmDirectory.h"
 
diff --git a/Source/cmClassFile.h b/Source/cmClassFile.h
index 307d13c..4004839 100644
--- a/Source/cmClassFile.h
+++ b/Source/cmClassFile.h
@@ -13,39 +13,66 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmClassFile a structure that represents a class loaded from 
- * a makefile.
- */
 #ifndef cmClassFile_h
 #define cmClassFile_h
-#include "cmStandardIncludes.h"
 
+#include "cmStandardIncludes.h"
 
-struct cmClassFile
+/** \class cmClassFile
+ * \brief Represent a class loaded from a makefile.
+ *
+ * cmClassFile is represents a class loaded from 
+ * a makefile.
+ */
+class cmClassFile
 {
+public:
+  /**
+   * Construct instance as a concrete class with both a
+   * .h and .cxx file.
+   */
   cmClassFile()
     {
-      m_AbstractClass = false;
-      m_HeaderFileOnly = false;
+    m_AbstractClass = false;
+    m_HeaderFileOnly = false;
     }
   
   /**
    * 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.
+   * the file should be in.  Various extensions are tried on 
+   * the name (e.g., .cxx, .cpp) in the directory to find the actual file.
    */
   void SetName(const char* name, const char* dir);
+
   /**
-   * print the structure to cout
+   * Print the structure to std::cout.
    */
   void Print();
 
-  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
+  /**
+   * Indicate whether the class is abstract (non-instantiable).
+   */
+  bool m_AbstractClass;
+
+  /**
+   * Indicate whether this class is defined with only the header file.
+   */
+  bool m_HeaderFileOnly;
+
+  /**
+   * The full path to the file.
+   */
+  std::string m_FullPath;
+
+  /**
+   * The file name associated with stripped off directory and extension.
+   * (In most cases this is the name of the class.)
+   */
+  std::string m_ClassName;
+
+  /**
+   * The dependencies of this class are gathered here.
+   */
   std::vector<std::string> m_Depends;
 };
 
diff --git a/Source/cmDSWMakefile.cxx b/Source/cmDSWMakefile.cxx
index fb5c718..703c4b5 100644
--- a/Source/cmDSWMakefile.cxx
+++ b/Source/cmDSWMakefile.cxx
@@ -70,7 +70,7 @@ cmDSWMakefile
     {
     // Create a new cmDSPMakefile to read the currentDir CMakeLists.txt file
     cmMSProjectGenerator* pg = new cmMSProjectGenerator;
-    pg->SetBuildDSP();
+    pg->BuildDSPOff();
     cmMakefile* mf = new cmMakefile;
     mf->SetMakefileGenerator(pg);
     // add it to the vector
diff --git a/Source/cmDSWMakefile.h b/Source/cmDSWMakefile.h
index 6a476b7..b2d4fe8 100644
--- a/Source/cmDSWMakefile.h
+++ b/Source/cmDSWMakefile.h
@@ -13,22 +13,33 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmDSWMakefile - class to write a microsoft DSW file.
- */
 #ifndef cmDSWMakefile_h
 #define cmDSWMakefile_h
+
 #include "cmStandardIncludes.h"
 #include "cmMakefile.h"
 
 class cmDSPMakefile;
 class cmMSProjectGenerator;
 
+/** \class cmDSWMakefile
+ * \brief Write a Microsoft Visual C++ DSW (workspace) file.
+ *
+ * cmDSWMakefile produces a Microsoft Visual C++ DSW (workspace) file.
+ */
 class cmDSWMakefile 
 {
 public:
+  /**
+   * Constructor.
+   */
   cmDSWMakefile(cmMakefile*);
+  
+  /**
+   * Generate the DSW workspace file.
+   */
   virtual void OutputDSWFile();
+
 private:
   void FindAllCMakeListsFiles(const char* subdir,
 			      std::vector<cmMSProjectGenerator*>&);
diff --git a/Source/cmDSWWriter.cxx b/Source/cmDSWWriter.cxx
index fb5c718..703c4b5 100644
--- a/Source/cmDSWWriter.cxx
+++ b/Source/cmDSWWriter.cxx
@@ -70,7 +70,7 @@ cmDSWMakefile
     {
     // Create a new cmDSPMakefile to read the currentDir CMakeLists.txt file
     cmMSProjectGenerator* pg = new cmMSProjectGenerator;
-    pg->SetBuildDSP();
+    pg->BuildDSPOff();
     cmMakefile* mf = new cmMakefile;
     mf->SetMakefileGenerator(pg);
     // add it to the vector
diff --git a/Source/cmDSWWriter.h b/Source/cmDSWWriter.h
index 6a476b7..b2d4fe8 100644
--- a/Source/cmDSWWriter.h
+++ b/Source/cmDSWWriter.h
@@ -13,22 +13,33 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmDSWMakefile - class to write a microsoft DSW file.
- */
 #ifndef cmDSWMakefile_h
 #define cmDSWMakefile_h
+
 #include "cmStandardIncludes.h"
 #include "cmMakefile.h"
 
 class cmDSPMakefile;
 class cmMSProjectGenerator;
 
+/** \class cmDSWMakefile
+ * \brief Write a Microsoft Visual C++ DSW (workspace) file.
+ *
+ * cmDSWMakefile produces a Microsoft Visual C++ DSW (workspace) file.
+ */
 class cmDSWMakefile 
 {
 public:
+  /**
+   * Constructor.
+   */
   cmDSWMakefile(cmMakefile*);
+  
+  /**
+   * Generate the DSW workspace file.
+   */
   virtual void OutputDSWFile();
+
 private:
   void FindAllCMakeListsFiles(const char* subdir,
 			      std::vector<cmMSProjectGenerator*>&);
diff --git a/Source/cmDirectory.h b/Source/cmDirectory.h
index e2b92c3..3400f3d 100644
--- a/Source/cmDirectory.h
+++ b/Source/cmDirectory.h
@@ -18,20 +18,19 @@
 
 #include "cmStandardIncludes.h"
 #include "cmSystemTools.h"
+
 /** \class cmDirectory
  * \brief Portable directory/filename traversal.
  * 
  * cmDirectory provides a portable way of finding the names of the files
  * in a system directory.
  *
- * cmDirectory works with windows and unix only.
+ * cmDirectory currently works with Windows and Unix operating systems.
  */
 
-
 class cmDirectory 
 {
 public:
-  
   /**
    * Load the specified directory and load the names of the files
    * in that directory. 0 is returned if the directory can not be 
@@ -52,7 +51,7 @@ public:
 private:
   std::vector<std::string> m_Files; // Array of Files
   std::string m_Path;               // Path to Open'ed directory
-}; // End Class: cmDirectory
 
+}; // End Class: cmDirectory
   
 #endif
diff --git a/Source/cmFindProgramRule.h b/Source/cmFindProgramRule.h
index 10ad46e..a94bb38 100644
--- a/Source/cmFindProgramRule.h
+++ b/Source/cmFindProgramRule.h
@@ -24,7 +24,8 @@
  *
  * cmFindProgramRule is used to define a CMake variable
  * that specifies an executable program. The rule searches 
- * for a given file in a list of directories.
+ * in the current path (e.g., PATH environment variable) for
+ * an executable that matches one of the supplied names.
  */
 class cmFindProgramRule : public cmRuleMaker
 {
@@ -74,7 +75,7 @@ public:
   virtual const char* FullDocumentation()
     {
     return
-      "FIND_PROGRAM(NAME try1 try2 ...)";
+      "FIND_PROGRAM(NAME executable1 executable2 ...)";
     }
 };
 
diff --git a/Source/cmMSProjectGenerator.cxx b/Source/cmMSProjectGenerator.cxx
index f029035..c3b38f0 100644
--- a/Source/cmMSProjectGenerator.cxx
+++ b/Source/cmMSProjectGenerator.cxx
@@ -6,7 +6,7 @@ cmMSProjectGenerator::cmMSProjectGenerator()
 {
   m_DSWMakefile = 0;
   m_DSPMakefile = 0;
-  SetBuildDSW();
+  BuildDSWOn();
 }
 
 void cmMSProjectGenerator::GenerateMakefile()
diff --git a/Source/cmMSProjectGenerator.h b/Source/cmMSProjectGenerator.h
index 3272a42..e572db7 100644
--- a/Source/cmMSProjectGenerator.h
+++ b/Source/cmMSProjectGenerator.h
@@ -13,28 +13,62 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmMSProjectGenerator - class to write a microsoft DSW file.
- */
 #ifndef cmMSProjectGenerator_h
 #define cmMSProjectGenerator_h
+
 #include "cmStandardIncludes.h"
 #include "cmMakefileGenerator.h"
 
 class cmDSPMakefile;
 class cmDSWMakefile;
 
-
+/** \class cmMSProjectGenerator
+ * \brief Write a Microsoft Visual C++ DSP (project) file.
+ *
+ * cmMSProjectGenerator produces a Microsoft Visual C++ DSP (project) file.
+ */
 class cmMSProjectGenerator : public cmMakefileGenerator
 {
 public:
+  /**
+   * Constructor sets the generation of DSW files on.
+   */
   cmMSProjectGenerator();
+
+  /**
+   * Destructor.
+   */
   ~cmMSProjectGenerator();
+
+  /**
+   * Produce the makefile (in this case a Microsoft Visual C++ project).
+   */
   virtual void GenerateMakefile();
-  void SetBuildDSP() { m_BuildDSW = false;}
-  void SetBuildDSW() { m_BuildDSW = true;}
-  cmDSWMakefile* GetDSWMakefile() { return m_DSWMakefile;}
-  cmDSPMakefile* GetDSPMakefile() { return m_DSPMakefile;}
+
+  /**
+   * Turn off the generation of a Microsoft Visual C++ DSP file.
+   */
+  void BuildDSPOff() 
+    {m_BuildDSW = false;}
+
+  /**
+   * Turn on the generation of a Microsoft Visual C++ DSW file.
+   */
+  void BuildDSWOn() 
+    {m_BuildDSW = true;}
+
+  /**
+   * Retrieve a pointer to a cmDSWMakefile instance.
+   */
+  cmDSWMakefile* GetDSWMakefile() 
+    {return m_DSWMakefile;}
+
+  /**
+   * Retrieve a pointer to a cmDSPMakefile instance.
+   */
+  cmDSPMakefile* GetDSPMakefile() 
+    {return m_DSPMakefile;}
+
 private:
   cmDSWMakefile* m_DSWMakefile;
   cmDSPMakefile* m_DSPMakefile;
diff --git a/Source/cmMakeDepend.h b/Source/cmMakeDepend.h
index e383910..041fc18 100644
--- a/Source/cmMakeDepend.h
+++ b/Source/cmMakeDepend.h
@@ -13,9 +13,6 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmMakeDepend 
- */
 #ifndef cmMakeDepend_h
 #define cmMakeDepend_h
 
@@ -24,39 +21,59 @@
 #include "cmRegularExpression.h"
 #include "cmStandardIncludes.h"
 
-
-// This structure stores the depend information 
-// for a single source file
+/** \class cmDependInformation
+ * \brief Store dependency information for a single source file.
+ *
+ * This structure stores the depend information for a single source file.
+ */
 struct cmDependInformation
 {
+  /**
+   * Construct with dependency generation marked not done; instance
+   * not placed in cmMakefile's list.
+   */
   cmDependInformation() 
     {
-      m_DependDone = false;
-      m_ClassFileIndex = -1;
+    m_DependDone = false;
+    m_ClassFileIndex = -1;
     }
-// index into m_DependInformation array of cmMakeDepend 
-// class, represents the files that this file depends on
+
+  /**
+   * A list of indices into the m_DependInformation array of cmMakeDepend.
+   * The index represents the files that this file depends on.
+   */
   std::vector<int> m_Indices;	
 
-// full path to file
+  /**
+   * Full path to this file.
+   */
   std::string m_FullPath;	
 
-// name as include directive uses
+  /**
+   * Name that the include directive uses.
+   */
   std::string m_IncludeName;
 
-// refers back to the index of the  cmMakefile's array
-// of cmClassFile objects which this class class describes,
-// -1 for files not in the array
+  /**
+   * The index into the cmMakefile::m_Classes list.
+   * The index value of -1 indicates that it is not in the list.
+   */
   int m_ClassFileIndex;	
   
-// flag to determine if depends have
-// been done for this file
+  /**
+   * This flag indicates whether dependency checking has been
+   * performed for this file.
+   */
   bool m_DependDone;
   
-// function to add the depends of another file to this one
+  /**
+   * This method adds the dependencies of another file to this one.
+   */
   void MergeInfo(cmDependInformation*);
   
-// remove duplicate depends from the index list
+  /**
+   * This method removes duplicate depends from the index list.
+   */
   void RemoveDuplicateIndices();
 };
 
@@ -66,43 +83,60 @@ struct cmDependInformation
 class cmMakeDepend
 {
 public:
+  /**
+   * Construct the object with verbose turned off.
+   */
   cmMakeDepend();
+
+  /**
+   * Destructor.
+   */
   ~cmMakeDepend();
   
   /** 
    * Set the makefile that is used as a source of classes.
    */
   void SetMakefile(cmMakefile* makefile); 
+
   /** 
    * Generate the depend information
    */
   void DoDepends();
+
   /** 
    * Set a regular expression that include files must match
-   * in order to be considered as part of the depend information
+   * in order to be considered as part of the depend information.
    */
   void SetIncludeRegularExpression(const char* regex);
+
   /**
-   * Add a directory to the search path for include files
+   * Add a directory to the search path for include files.
    */
   void AddSearchPath(const char*);
+
 private: 
+  /**
+   * Add a source file to the search path.
+   */
   void AddFileToSearchPath(const char* filepath);
+
   /**
    * Find the index into the m_DependInformation array
-   * that matches the given m_IncludeName
+   * that matches the given m_IncludeName.
    */
   int FindInformation(const char* includeName);
+
   /**
-   * Compute the depend information for this class
+   * Compute the depend information for this class.
    */
   void Depend(cmDependInformation* info);
+
   /** 
    * Find the full path name for the given file name.
-   * This uses the include directories
+   * This uses the include directories.
    */
   std::string FullPath(const char*);
-private:
+
   cmMakefile* m_Makefile;
   bool m_Verbose;
   cmRegularExpression m_IncludeFileRegularExpression;
diff --git a/Source/cmMakefile.h b/Source/cmMakefile.h
index c377e90..001ba4a 100644
--- a/Source/cmMakefile.h
+++ b/Source/cmMakefile.h
@@ -13,162 +13,293 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmMakefile - used to parse and store the contents of a
- * CMakeLists.txt makefile in memory.
- */
 #ifndef cmMakefile_h
 #define cmMakefile_h
+
 #include "cmStandardIncludes.h"
 #include "cmClassFile.h"
 #include "cmSystemTools.h"
+
 class cmRuleMaker;
 class cmMakefileGenerator;
 
-
+/** \class cmMakefile
+ * \brief Process the input CMakeLists.txt file.
+ *
+ * Process and store into memory the input CMakeLists.txt file.
+ * Each CMakeLists.txt file is parsed and the rules found there
+ * are added into the build process.
+ */
 class cmMakefile
 {
 public:
+  /**
+   * Construct an empty makefile.
+   */
   cmMakefile();
+
+  /**
+   * Destructor.
+   */
   ~cmMakefile();
-  // Parse a CMakeLists.txt file
+
+  /**
+   * Read and parse a CMakeLists.txt file.
+   */
   bool ReadMakefile(const char* makefile, bool inheriting = false); 
-  // Add a wrap generator 
+
+  /**
+   * Add a wrapper generator.
+   */
   void AddRuleMaker(cmRuleMaker* );
-  // Set the make file 
+
+  /**
+   * Specify the makefile generator. This is platform/compiler
+   * dependent, although the interface is through a generic
+   * superclass.
+   */
   void SetMakefileGenerator(cmMakefileGenerator*);
-  // Generate the output file
+
+  /**
+   * Produce the output makefile.
+   */
   void GenerateMakefile();
   
-  // Print useful stuff to stdout
+  /**
+   * Print the object state to std::cout.
+   */
   void Print();
   
-  // cmRuleMaker interfaces
+  /**
+   * Add a custom rule to the build.
+   */
   void AddCustomRule(const char* source,
                      const char* result,
                      const char* command,
                      std::vector<std::string>& depends);
+  /**
+   * Add a define flag to the build.
+   */
   void AddDefineFlag(const char* definition);
+
+  /**
+   * Add an executable to the build.
+   */
   void AddExecutable(cmClassFile&);
+
+  /**
+   * Add a link library to the build.
+   */
   void AddLinkLibrary(const char*);
+
+  /**
+   * Add a link directory to the build.
+   */
   void AddLinkDirectory(const char*);
+
+  /**
+   * Add a subdirectory to the build.
+   */
   void AddSubDirectory(const char*);
+
+  /**
+   * Add an include directory to the build.
+   */
   void AddIncludeDirectory(const char*);
+
+  /**
+   * Add a variable definition to the build. This variable
+   * can be used in CMake to refer to lists, directories, etc.
+   */
   void AddDefinition(const char* name, const char* value);
+
+  /**
+   * Specify the name of the project for this build.
+   */
   void SetProjectName(const char*);
+
+  /**
+   * Get the name of the project for this build.
+   */
+  const char* GetProjectName()
+    {
+    return m_ProjectName.c_str();
+    }
+  
+  /**
+   * Set the name of the library.
+   */
   void SetLibraryName(const char*);
+
+  /**
+   * Add a class/source file to the build.
+   */
   void AddClass(cmClassFile& );
+
+  /**
+   * Add an auxiliary directory to the build.
+   */
   void AddExtraDirectory(const char* dir);
   
-  // Set the home directory for the project
+  /**
+   * Specify the home directory for the build.
+   */
   void SetHomeDirectory(const char* dir) 
     {
-      m_cmHomeDirectory = dir;
-      cmSystemTools::ConvertToUnixSlashes(m_cmHomeDirectory);
+    m_cmHomeDirectory = dir;
+    cmSystemTools::ConvertToUnixSlashes(m_cmHomeDirectory);
     }
+
+  /**
+   * Get the home directory for the build.
+   */
   const char* GetHomeDirectory() 
     {
-      return m_cmHomeDirectory.c_str();
+    return m_cmHomeDirectory.c_str();
     }
-  // Set the current directory in the project
+
+  /**
+   * Set the current directory in the project.
+   */
   void SetCurrentDirectory(const char* dir) 
     {
-      m_cmCurrentDirectory = dir;
+    m_cmCurrentDirectory = dir;
     }
+
+  /**
+   * Get the current directory in the project.
+   */
   const char* GetCurrentDirectory() 
     {
-      return m_cmCurrentDirectory.c_str();
+    return m_cmCurrentDirectory.c_str();
     }
-  // Set the name of the library that is built by this makefile
+
+  /**
+   * Specify the name of the library that is built by this makefile.
+   */
   const char* GetLibraryName()
     {
-      return m_LibraryName.c_str();
+    return m_LibraryName.c_str();
     }
 
-  const char* GetProjectName()
-    {
-      return m_ProjectName.c_str();
-    }
-  
-  // Set the name of the library that is built by this makefile
+  /**
+   * Set the name of the library that is built by this makefile.
+   */
   void SetOutputDirectory(const char* lib)
     {
-      m_OutputDirectory = lib;
+    m_OutputDirectory = lib;
     }
+
+  /**
+   * Get the name of the library that is built by this makefile.
+   */
   const char* GetOutputDirectory()
     {
-      return m_OutputDirectory.c_str();
+    return m_OutputDirectory.c_str();
     }
-  
-  // Set the name of the library that is built by this makefile
+
+  /**
+   * Set the name of the current output directory.
+   */
   void SetOutputHomeDirectory(const char* lib)
     {
-      m_OutputHomeDirectory = lib;
+    m_OutputHomeDirectory = lib;
     }
+
+  /**
+   * Get the name of the current output directory.
+   */
   const char* GetOutputHomeDirectory()
     {
-      return m_OutputHomeDirectory.c_str();
+    return m_OutputHomeDirectory.c_str();
     }
+
+  /**
+   * Get a list of the build subdirectories.
+   */
   const std::vector<std::string>& GetSubDirectories()
     { 
-      return m_SubDirectories;
+    return m_SubDirectories;
     }
-  
+
+  /**
+   * Return a boolean flag indicating whether the build generates
+   * any executables.
+   */
   bool HasExecutables() 
     {
-      return m_Executables;
+    return m_Executables;
     }
-  
+
+  /**
+   * Get a list of include directories in the build.
+   */
   std::vector<std::string>& GetIncludeDirectories()
     { 
-      return m_IncludeDirectories;
+    return m_IncludeDirectories;
     }
-  
+
+  /**
+   * Get a list of link directories in the build.
+   */
   std::vector<std::string>& GetLinkDirectories()
     { 
-      return m_LinkDirectories;
+    return m_LinkDirectories;
     }
   
+  /**
+   * Get a list of link libraries in the build.
+   */
   std::vector<std::string>& GetLinkLibraries()
     { 
-      return m_LinkLibraries;
+    return m_LinkLibraries;
     }
-  
+
+  /**
+   * Get a list of Win32 link libraries in the build.
+   */
   std::vector<std::string>& GetLinkLibrariesWin32()
     { 
-      return m_LinkLibrariesWin32;
+    return m_LinkLibrariesWin32;
     }
   
+  /**
+   * Get a list of Unix link libraries in the build.
+   */
   std::vector<std::string>& GetLinkLibrariesUnix()
     { 
-      return m_LinkLibrariesUnix;
+    return m_LinkLibrariesUnix;
     }
-  std::vector<cmClassFile>& GetClasses(){ return  m_Classes;}
+
+  /**
+   * Return a list of source files in this makefile.
+   */
+  std::vector<cmClassFile>& GetClasses()
+    {return  m_Classes;}
+
+  /**
+   * Obtain a list of auxiliary source directories.
+   */
   std::vector<std::string>& GetAuxSourceDirectories()
-    { return m_AuxSourceDirectories; }
-  std::vector<std::string>& GetMakeVerbatim() 
-    { return m_MakeVerbatim;}
-  const char* GetDefinition(const char*);
+    {return m_AuxSourceDirectories;}
 
-  const char* GetDefineFlags()
-    { return m_DefineFlags.c_str();}
+  /**
+   * Do not use this.
+   */
+  std::vector<std::string>& GetMakeVerbatim() 
+    {return m_MakeVerbatim;}
 
-private:
-   /**
-   * Look for CMakeLists.txt files to parse in dir,
-   * then in dir's parents, until the SourceHome directory
-   * is found.
+  /**
+   * Given a variable name, return its value (as a string).
    */
-  void ParseDirectory(const char* dir);
+  const char* GetDefinition(const char*);
+
   /**
-   * Parse a file for includes links and libs
+   * Get a list of preprocessor define flags.
    */
-  void ExpandVaribles();
-  void ReadClasses(std::ifstream& fin, bool t);
-  friend class cmMakeDepend;	// make depend needs direct access 
-				// to the m_Classes array 
-  void PrintStringVector(const char* s, std::vector<std::string>& v);
-  void AddDefaultRules();
+  const char* GetDefineFlags()
+    {return m_DefineFlags.c_str();}
+
 protected:
   bool m_Executables;
   std::string m_Prefix;
@@ -203,6 +334,26 @@ protected:
   StringRuleMakerMap m_RuleMakers;
   std::vector<cmRuleMaker*> m_UsedRuleMakers;
   cmMakefileGenerator* m_MakefileGenerator;
+  
+private:
+   /**
+   * Look for CMakeLists.txt files to parse in dir,
+   * then in dir's parents, until the SourceHome directory
+   * is found.
+   */
+  void ParseDirectory(const char* dir);
+
+  /**
+   * Parse a file for includes links and libs
+   */
+  void ExpandVaribles();
+
+  void ReadClasses(std::ifstream& fin, bool t);
+  friend class cmMakeDepend;	// make depend needs direct access 
+				// to the m_Classes array 
+  void PrintStringVector(const char* s, std::vector<std::string>& v);
+  void AddDefaultRules();
+  
 };
 
 
diff --git a/Source/cmMakefileGenerator.h b/Source/cmMakefileGenerator.h
index f676cc6..2ab50e4 100644
--- a/Source/cmMakefileGenerator.h
+++ b/Source/cmMakefileGenerator.h
@@ -1,18 +1,47 @@
-#ifndef cmMakeFileGenerator_h
-#define cmMakeFileGenerator_h
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
+#ifndef cmMakefileGenerator_h
+#define cmMakefileGenerator_h
 
 #include "cmStandardIncludes.h"
 
 class cmMakefile;
-struct cmClassFile;
+class cmClassFile;
 
+/** \class cmMakefileGenerator
+ * \brief Provide an abstract interface for classes generating makefiles.
+ *
+ * Subclasses of this abstract class generate makefiles for various
+ * platforms.
+ */
 class cmMakefileGenerator
 {
 public:
-  // use the m_Makefile and the m_CustomRules and m_ExtraSourceFiles
-  // to generate the makefile
-  virtual void GenerateMakefile() = 0;
+  /**
+   * Set the cmMakefile instance from which to generate the makefile.
+   */
   void SetMakefile(cmMakefile*);
+
+  /**
+   * Generate the makefile using the m_Makefile, m_CustomRules, 
+   * and m_ExtraSourceFiles. All subclasses of cmMakefileGenerator
+   * must implement this method.
+   */
+  virtual void GenerateMakefile() = 0;
+
 protected:
   cmMakefile* m_Makefile;
 };
diff --git a/Source/cmRegularExpression.cxx b/Source/cmRegularExpression.cxx
index f97fc02..bf2b529 100644
--- a/Source/cmRegularExpression.cxx
+++ b/Source/cmRegularExpression.cxx
@@ -1,3 +1,18 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
 //
 // Copyright (C) 1991 Texas Instruments Incorporated.
 //
@@ -16,111 +31,12 @@
 // Updated: MBN 12/15/89  Sprinkled "const" qualifiers all over the place!
 // Updated: DLS 03/22/91  New lite version
 //
-// This  is the header file  for the regular  expression class.   An object of
-// this class contains a regular expression,  in  a special "compiled" format.
-// This  compiled format consists  of  several slots   all kept as the objects
-// private data.  The cmRegularExpression class  provides a convenient  way  to  represent
-// regular  expressions.  It makes it easy   to search  for  the  same regular
-// expression in many different strings without having to  compile a string to
-// regular expression format more than necessary.
-//
-// A regular  expression allows a programmer to  specify complex patterns that
-// can be searched for  and  matched against the  character string of a String
-// object.  In  its  simplest case, a   regular expression  is a  sequence  of
-// characters with which you can search for exact character matches.  However,
-// many times you may not know the exact sequence you want to find, or you may
-// only want to find a match at the beginning or end of  a String.  The cmRegularExpression
-// object  allows specification of  such patterns by  utilizing the  following
-// regular  expression  meta-characters   (note   that  more  one  of    these
-// meta-characters  can  be used in a single  regular  expression in  order to
-// create complex search patterns):
-//
-//         ^    Match at beginning of line
-//         $    Match at end of line
-//         .    Match any single character
-//         [ ]  Match any one character inside the brackets
-//         [^ ] Match any character NOT inside the brackets
-//         -    Match any character in range on either side of dash
-//         *    Match preceding pattern zero or more times
-//         +    Match preceding pattern one or more times
-//         ?    Match preceding pattern zero or once only
-//         ()   Save a matched expression and use it in a further match.
-//
-// There are three constructors for cmRegularExpression.  One  just creates an empty cmRegularExpression
-// object.  Another creates a cmRegularExpression object  and initializes it with a regular
-// expression  that is given  in  the form of a   char*.   The  third  takes a
-// reference  to  a cmRegularExpression  object    as an  argument    and creates an object
-// initialized with the information from the given cmRegularExpression object.
-//
-// The  find  member function  finds   the  first  occurence   of  the regualr
-// expression of that object in the string given to find as an argument.  Find
-// returns a boolean, and  if true,  mutates  the private  data appropriately.
-// Find sets pointers to the beginning and end of  the thing last  found, they
-// are pointers into the actual string  that was searched.   The start and end
-// member functions return indicies  into the searched string that  correspond
-// to the beginning   and  end pointers  respectively.   The    compile member
-// function takes a char* and puts the  compiled version of the char* argument
-// into the object's private data fields.  The == and  != operators only check
-// the  to see  if   the compiled  regular  expression   is the same, and  the
-// deep_equal functions also checks  to see if the  start and end pointers are
-// the same.  The is_valid  function returns false if  program is set to NULL,
-// (i.e. there is no valid compiled exression).  The set_invalid function sets
-// the  program to NULL  (Warning: this deletes the compiled  expression). The
-// following examples may help clarify regular expression usage:
-//
-//   *  The regular expression  "^hello" matches  a "hello"  only at  the
-//      beginning of a  line.  It would match "hello  there" but not "hi,
-//      hello there".
-//
-//   *  The regular expression "long$" matches a  "long"  only at the end
-//      of a line. It would match "so long\0", but not "long ago".
-//
-//   *  The regular expression "t..t..g"  will match anything that  has a
-//      "t" then any two characters, another "t", any  two characters and
-//      then a "g".   It will match  "testing", or "test again" but would
-//      not match "toasting"
-//
-//   *  The regular  expression "[1-9ab]" matches any  number one through
-//      nine, and the characters  "a" and  "b".  It would match "hello 1"
-//      or "begin", but would not match "no-match".
-//
-//   *  The  regular expression "[^1-9ab]"  matches any character that is
-//      not a number one  through nine, or  an "a" or "b".   It would NOT
-//      match "hello 1" or "begin", but would match "no-match".
-//
-//   *  The regular expression "br* " matches  something that begins with
-//      a "b", is followed by zero or more "r"s, and ends in a space.  It
-//      would match "brrrrr ", and "b ", but would not match "brrh ".
-//
-//   *  The regular expression "br+ " matches something  that begins with
-//      a "b", is followed by one or more "r"s, and ends in  a space.  It
-//      would match "brrrrr ",  and  "br ", but would not  match "b  " or
-//      "brrh ".
-//
-//   *  The regular expression "br? " matches  something that begins with
-//      a "b", is followed by zero or one "r"s, and ends in  a space.  It
-//      would  match  "br ", and "b  ", but would not match  "brrrr "  or
-//      "brrh ".
-//
-//   *  The regular expression "(..p)b" matches  something ending with pb
-//      and beginning with whatever the two characters before the first p
-//      encounterd in the line were.  It would find  "repb" in "rep drepa
-//      qrepb".  The regular expression "(..p)a"  would find "repa qrepb"
-//      in "rep drepa qrepb"
-//
-//   *  The regular expression "d(..p)" matches something ending  with p,
-//      beginning with d, and having  two characters  in between that are
-//      the same as the two characters before  the first p  encounterd in
-//      the line.  It would match "drepa qrepb" in "rep drepa qrepb".
-//
 
 #include "cmRegularExpression.h"	// Include class specification 
 #include "cmStandardIncludes.h"
 #include <stdio.h>
 
-
 // cmRegularExpression -- Copies the given regular expression.
-
 cmRegularExpression::cmRegularExpression (const cmRegularExpression& rxp) {
   int ind; 
   this->progsize = rxp.progsize;		// Copy regular expression size
@@ -144,10 +60,8 @@ cmRegularExpression::cmRegularExpression (const cmRegularExpression& rxp) {
   this->regmlen = rxp.regmlen;			// Copy remaining private data
 }
 
-
 // operator== -- Returns true if two regular expressions have the same
 // compiled program for pattern matching.
-
 bool cmRegularExpression::operator== (const cmRegularExpression& rxp) const {
   if (this != &rxp) {				// Same address?
     int ind = this->progsize;			// Get regular expression size
@@ -918,8 +832,9 @@ void         regdump ();
 static char* regprop ();
 #endif
 
-bool cmRegularExpression::find (std::string const& s) {
-return find(s.c_str());
+bool cmRegularExpression::find (std::string const& s) 
+{
+  return find(s.c_str());
 }
 
 
diff --git a/Source/cmRegularExpression.h b/Source/cmRegularExpression.h
index b713de4..0628e32 100644
--- a/Source/cmRegularExpression.h
+++ b/Source/cmRegularExpression.h
@@ -13,7 +13,7 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/// Original Copyright notice:
+// Original Copyright notice:
 // Copyright (C) 1991 Texas Instruments Incorporated.
 //
 // Permission is granted to any individual or institution to use, copy, modify,
@@ -24,11 +24,13 @@
 // Texas Instruments Incorporated provides this software "as is" without
 // express or implied warranty.
 //
-// .LIBRARY vbl
-// .HEADER Basics Package
-// .INCLUDE cmRegularExpression.h
-// .FILE cmRegularExpression.cxx
+// Created: MNF 06/13/89  Initial Design and Implementation
+// Updated: LGO 08/09/89  Inherit from Generic
+// Updated: MBN 09/07/89  Added conditional exception handling
+// Updated: MBN 12/15/89  Sprinkled "const" qualifiers all over the place!
+// Updated: DLS 03/22/91  New lite version
 //
+
 #ifndef cmRegularExpression_h
 #define cmRegularExpression_h
 
@@ -36,83 +38,225 @@
 
 const int NSUBEXP = 10;
 
-//: Pattern matching with regular expressions
-//  A regular expression allows a programmer to specify  complex
-//  patterns  that  can  be searched for and matched against the
-//  character string of a string object. In its simplest form, a
-//  regular  expression  is  a  sequence  of  characters used to
-//  search for exact character matches. However, many times  the
-//  exact  sequence to be found is not known, or only a match at
-//  the beginning or end of a string is desired. The vbl  regu-
-//  lar  expression  class implements regular expression pattern
-//  matching as is found and implemented in many  UNIX  commands
-//  and utilities.
-//
-//  Example: The perl code
-//  
-//     $filename =~ m"([a-z]+)\.cc";
-//     print $1;
-//     
-//  Is written as follows in C++
-//
-//     vbl_reg_exp re("([a-z]+)\\.cc");
-//     re.find(filename);
-//     cerr << re.match(1);
-//
-//
-//  The regular expression class provides a convenient mechanism
-//  for  specifying  and  manipulating  regular expressions. The
-//  regular expression object allows specification of such  pat-
-//  terns  by using the following regular expression metacharac-
-//  ters:
-// 
-//   ^        Matches at beginning of a line
-//
-//   $        Matches at end of a line
-//
-//  .         Matches any single character
-//
-//  [ ]       Matches any character(s) inside the brackets
-//
-//  [^ ]      Matches any character(s) not inside the brackets
-//
-//   -        Matches any character in range on either side of a dash
-//
-//   *        Matches preceding pattern zero or more times
-//
-//   +        Matches preceding pattern one or more times
-//
-//   ?        Matches preceding pattern zero or once only
-//
-//  ()        Saves a matched expression and uses it in a  later match
-// 
-//  Note that more than one of these metacharacters can be  used
-//  in  a  single  regular expression in order to create complex
-//  search patterns. For example, the pattern [^ab1-9]  says  to
-//  match  any  character  sequence that does not begin with the
-//  characters "ab"  followed  by  numbers  in  the  series  one
-//  through nine.
-//
-class cmRegularExpression {
+/** \class cmRegularExpression
+ * \brief Implements pattern matching with regular expressions.
+ *
+ * This is the header file for the regular expression class.  An object of
+ * this class contains a regular expression, in a special "compiled" format.
+ * This compiled format consists of several slots all kept as the objects
+ * private data.  The cmRegularExpression class provides a convenient way to
+ * represent regular expressions.  It makes it easy to search for the same
+ * regular expression in many different strings without having to compile a
+ * string to regular expression format more than necessary.
+ *
+ * This class implements pattern matching via regular expressions.
+ * A regular expression allows a programmer to specify  complex
+ * patterns  that  can  be searched for and matched against the
+ * character string of a string object. In its simplest form, a
+ * regular  expression  is  a  sequence  of  characters used to
+ * search for exact character matches. However, many times  the
+ * exact  sequence to be found is not known, or only a match at
+ * the beginning or end of a string is desired. The vbl  regu-
+ * lar  expression  class implements regular expression pattern
+ * matching as is found and implemented in many  UNIX  commands
+ * and utilities.
+ *
+ * Example: The perl code
+ * 
+ *    $filename =~ m"([a-z]+)\.cc";
+ *    print $1;
+ *    
+ * Is written as follows in C++
+ *
+ *    vbl_reg_exp re("([a-z]+)\\.cc");
+ *    re.find(filename);
+ *    cerr << re.match(1);
+ *
+ *
+ * The regular expression class provides a convenient mechanism
+ * for  specifying  and  manipulating  regular expressions. The
+ * regular expression object allows specification of such  pat-
+ * terns  by using the following regular expression metacharac-
+ * ters:
+ *
+ *  ^        Matches at beginning of a line
+ *
+ *  $        Matches at end of a line
+ *
+ * .         Matches any single character
+ *
+ * [ ]       Matches any character(s) inside the brackets
+ *
+ * [^ ]      Matches any character(s) not inside the brackets
+ *
+ *  -        Matches any character in range on either side of a dash
+ *
+ *  *        Matches preceding pattern zero or more times
+ *
+ *  +        Matches preceding pattern one or more times
+ *
+ *  ?        Matches preceding pattern zero or once only
+ *
+ * ()        Saves a matched expression and uses it in a  later match
+ *
+ * Note that more than one of these metacharacters can be  used
+ * in  a  single  regular expression in order to create complex
+ * search patterns. For example, the pattern [^ab1-9]  says  to
+ * match  any  character  sequence that does not begin with the
+ * characters "ab"  followed  by  numbers  in  the  series  one
+ * through nine.
+ *
+ * There are three constructors for cmRegularExpression.  One just creates an
+ * empty cmRegularExpression object.  Another creates a cmRegularExpression
+ * object and initializes it with a regular expression that is given in the
+ * form of a char*.  The third takes a reference to a cmRegularExpression
+ * object as an argument and creates an object initialized with the
+ * information from the given cmRegularExpression object.
+ *
+ * The  find  member function  finds   the  first  occurence   of  the regualr
+ * expression of that object in the string given to find as an argument.  Find
+ * returns a boolean, and  if true,  mutates  the private  data appropriately.
+ * Find sets pointers to the beginning and end of  the thing last  found, they
+ * are pointers into the actual string  that was searched.   The start and end
+ * member functions return indicies  into the searched string that  correspond
+ * to the beginning   and  end pointers  respectively.   The    compile member
+ * function takes a char* and puts the  compiled version of the char* argument
+ * into the object's private data fields.  The == and  != operators only check
+ * the  to see  if   the compiled  regular  expression   is the same, and  the
+ * deep_equal functions also checks  to see if the  start and end pointers are
+ * the same.  The is_valid  function returns false if  program is set to NULL,
+ * (i.e. there is no valid compiled exression).  The set_invalid function sets
+ * the  program to NULL  (Warning: this deletes the compiled  expression). The
+ * following examples may help clarify regular expression usage:
+ *
+ *   *  The regular expression  "^hello" matches  a "hello"  only at  the
+ *      beginning of a  line.  It would match "hello  there" but not "hi,
+ *      hello there".
+ *
+ *   *  The regular expression "long$" matches a  "long"  only at the end
+ *      of a line. It would match "so long\0", but not "long ago".
+ *
+ *   *  The regular expression "t..t..g"  will match anything that  has a
+ *      "t" then any two characters, another "t", any  two characters and
+ *      then a "g".   It will match  "testing", or "test again" but would
+ *      not match "toasting"
+ *
+ *   *  The regular  expression "[1-9ab]" matches any  number one through
+ *      nine, and the characters  "a" and  "b".  It would match "hello 1"
+ *      or "begin", but would not match "no-match".
+ *
+ *   *  The  regular expression "[^1-9ab]"  matches any character that is
+ *      not a number one  through nine, or  an "a" or "b".   It would NOT
+ *      match "hello 1" or "begin", but would match "no-match".
+ *
+ *   *  The regular expression "br* " matches  something that begins with
+ *      a "b", is followed by zero or more "r"s, and ends in a space.  It
+ *      would match "brrrrr ", and "b ", but would not match "brrh ".
+ *
+ *   *  The regular expression "br+ " matches something  that begins with
+ *      a "b", is followed by one or more "r"s, and ends in  a space.  It
+ *      would match "brrrrr ",  and  "br ", but would not  match "b  " or
+ *      "brrh ".
+ *
+ *   *  The regular expression "br? " matches  something that begins with
+ *      a "b", is followed by zero or one "r"s, and ends in  a space.  It
+ *      would  match  "br ", and "b  ", but would not match  "brrrr "  or
+ *      "brrh ".
+ *
+ *   *  The regular expression "(..p)b" matches  something ending with pb
+ *      and beginning with whatever the two characters before the first p
+ *      encounterd in the line were.  It would find  "repb" in "rep drepa
+ *      qrepb".  The regular expression "(..p)a"  would find "repa qrepb"
+ *      in "rep drepa qrepb"
+ *
+ *   *  The regular expression "d(..p)" matches something ending  with p,
+ *      beginning with d, and having  two characters  in between that are
+ *      the same as the two characters before  the first p  encounterd in
+ *      the line.  It would match "drepa qrepb" in "rep drepa qrepb".
+ *
+ */
+class cmRegularExpression 
+{
 public:
-  inline cmRegularExpression ();			// cmRegularExpression with program=NULL
-  inline cmRegularExpression (char const*);	// cmRegularExpression with compiled char*
-  cmRegularExpression (cmRegularExpression const&);	// Copy constructor
-  inline ~cmRegularExpression();			// Destructor 
-
-  void compile (char const*);		// Compiles char* --> regexp
-  bool find (char const*);		// true if regexp in char* arg
-  bool find (std::string const&);		// true if regexp in char* arg
-  inline long start() const;		// Index to start of first find
-  inline long end() const;		// Index to end of first find
-
-  bool operator== (cmRegularExpression const&) const;	// Equality operator
-  inline bool operator!= (cmRegularExpression const&) const; // Inequality operator
-  bool deep_equal (cmRegularExpression const&) const;	// Same regexp and state?
+  /**
+   * Instantiate cmRegularExpression with program=NULL.
+   */
+  inline cmRegularExpression ();	
+
+  /**
+   * Instantiate cmRegularExpression with compiled char*.
+   */
+  inline cmRegularExpression (char const*);
   
-  inline bool is_valid() const;		// true if compiled regexp
-  inline void set_invalid();		// Invalidates regexp
-
+  /**
+   * Instantiate cmRegularExpression as a copy of another regular expression.
+   */
+  cmRegularExpression (cmRegularExpression const&);
+
+  /**
+   * Destructor.
+   */
+  inline ~cmRegularExpression();
+
+  /**
+   * Compile a regular expression into internal code
+   * for later pattern matching.
+   */
+  void compile (char const*);
+
+  /**
+   * Matches the regular expression to the given string.
+   * Returns true if found, and sets start and end indexes accordingly.
+   */
+  bool find (char const*);
+
+  /**
+   * Matches the regular expression to the given std string.
+   * Returns true if found, and sets start and end indexes accordingly.
+   */
+  bool find (std::string const&);		
+
+  /**
+   * Index to start of first find.
+   */
+  inline long start() const;
+
+  /**
+   * Index to end of first find.
+   */
+  inline long end() const;
+
+  /**
+   * Returns true if two regular expressions have the same
+   * compiled program for pattern matching.
+   */
+  bool operator== (cmRegularExpression const&) const;
+
+  /**
+   * Returns true if two regular expressions have different
+   * compiled program for pattern matching.
+   */
+  inline bool operator!= (cmRegularExpression const&) const;
+
+  /**
+   * Returns true if have the same compiled regular expressions
+   * and the same start and end pointers.
+   */
+  bool deep_equal (cmRegularExpression const&) const;
+  
+  /**
+   * True if the compiled regexp is valid.
+   */
+  inline bool is_valid() const;
+
+  /**
+   * Marks the regular expression as invalid.
+   */
+  inline void set_invalid();		
+
+  /**
+   * Destructor.
+   */
   // awf added
   int start(int n) const;
   int end(int n) const;
@@ -130,82 +274,98 @@ private:
   const char* searchstring;
 }; 
 
-// cmRegularExpression -- Creates an empty regular expression.
-
-inline cmRegularExpression::cmRegularExpression () { 
+/**
+ * Create an empty regular expression.
+ */
+inline cmRegularExpression::cmRegularExpression () 
+{ 
   this->program = NULL;
 }
 
-
-// cmRegularExpression -- Creates a regular expression from string s, and
-// compiles s.
-
-
-inline cmRegularExpression::cmRegularExpression (const char* s) {  
+/**
+ * Creates a regular expression from string s, and
+ * compiles s.
+ */
+inline cmRegularExpression::cmRegularExpression (const char* s) 
+{  
   this->program = NULL;
   compile(s);
 }
 
-// ~cmRegularExpression -- Frees space allocated for regular expression.
-
-inline cmRegularExpression::~cmRegularExpression () {
+/**
+ * Destroys and frees space allocated for the regular expression.
+ */
+inline cmRegularExpression::~cmRegularExpression () 
+{
 //#ifndef WIN32
   delete [] this->program;
 //#endif
 }
 
-// Start -- 
-
-inline long cmRegularExpression::start () const {
+/**
+ * Set the start position for the regular expression.
+ */
+inline long cmRegularExpression::start () const 
+{
   return(this->startp[0] - searchstring);
 }
 
 
-// End -- Returns the start/end index of the last item found.
-
-
-inline long cmRegularExpression::end () const {
+/**
+ * Returns the start/end index of the last item found.
+ */
+inline long cmRegularExpression::end () const 
+{
   return(this->endp[0] - searchstring);
 }
 
-
-// operator!= //
-
-inline bool cmRegularExpression::operator!= (const cmRegularExpression& r) const {
+/**
+ * Returns true if two regular expressions have different
+ * compiled program for pattern matching.
+ */
+inline bool cmRegularExpression::operator!= (const cmRegularExpression& r) const 
+{
   return(!(*this == r));
 }
 
-
-// is_valid -- Returns true if a valid regular expression is compiled
-// and ready for pattern matching.
-
-inline bool cmRegularExpression::is_valid () const {
+/**
+ * Returns true if a valid regular expression is compiled
+ * and ready for pattern matching.
+ */
+inline bool cmRegularExpression::is_valid () const 
+{
   return (this->program != NULL);
 }
 
 
-// set_invalid -- Invalidates regular expression.
-
-inline void cmRegularExpression::set_invalid () {
+inline void cmRegularExpression::set_invalid () 
+{
 //#ifndef WIN32
   delete [] this->program;
 //#endif
   this->program = NULL;
 }
 
-// -- Return start index of nth submatch. start(0) is the start of the full match.
+/**
+ * Return start index of nth submatch. start(0) is the start of the full match.
+ */
 inline int cmRegularExpression::start(int n) const
 {
   return this->startp[n] - searchstring;
 }
 
-// -- Return end index of nth submatch. end(0) is the end of the full match.
+
+/**
+ * Return end index of nth submatch. end(0) is the end of the full match.
+ */
 inline int cmRegularExpression::end(int n) const
 {
   return this->endp[n] - searchstring;
 }
 
-// -- Return nth submatch as a string.
+/**
+ * Return nth submatch as a string.
+ */
 inline std::string cmRegularExpression::match(int n) const
 {
   return std::string(this->startp[n], this->endp[n] - this->startp[n]);
diff --git a/Source/cmStandardIncludes.h b/Source/cmStandardIncludes.h
index 5a78e9b..3187f34 100644
--- a/Source/cmStandardIncludes.h
+++ b/Source/cmStandardIncludes.h
@@ -1,3 +1,22 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
+/**
+ * Include header files as a function of the build process, compiler,
+ * and operating system.
+ */
 #ifndef cmStandardIncludes_h
 #define cmStandardIncludes_h
 
diff --git a/Source/cmSystemTools.cxx b/Source/cmSystemTools.cxx
index 8e0eb57..c702ed6 100644
--- a/Source/cmSystemTools.cxx
+++ b/Source/cmSystemTools.cxx
@@ -79,13 +79,13 @@ bool cmSystemTools::FileExists(const char* filename)
 {
   struct stat fs;
   if (stat(filename, &fs) != 0) 
-  {
+    {
     return false;
-  }
+    }
   else
-  {
+    {
     return true;
-  }
+    }
 }
 
 
diff --git a/Source/cmSystemTools.h b/Source/cmSystemTools.h
index 4d98dc8..199d29c 100644
--- a/Source/cmSystemTools.h
+++ b/Source/cmSystemTools.h
@@ -13,14 +13,17 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmSystemTools - a collection of useful functions for CMake.
- */
 #ifndef cmSystemTools_h
 #define cmSystemTools_h
 
 #include "cmStandardIncludes.h"
 
+/** \class cmSystemTools
+ * \brief A collection of useful functions for CMake.
+ *
+ * cmSystemTools is a class that provides helper functions
+ * for the CMake build system.
+ */
 class cmSystemTools
 {
 public:
@@ -30,47 +33,54 @@ public:
    * prior to calling this function.  
    */
   static bool MakeDirectory(const char* path);
+
   /**
-   * Replace replace all occurances of the string in in
-   * souce string.
+   * Replace replace all occurances of the string in
+   * the source string.
    */
   static void ReplaceString(std::string& source,
                             const char* replace,
                             const char* with);
+
   /**
-   * Replace windows slashes with unix style slashes
+   * Replace Windows file system slashes with Unix-style slashes.
    */
   static void ConvertToUnixSlashes(std::string& path);
  
   /**
-   * Return true if a file exists
+   * Return true if a file exists in the current directory.
    */
   static bool FileExists(const char* filename);
+
   /**
-   * Return the number of times expression occurs in file in dir
+   * Return the number of times the given expression occurs in the file
+   * specified by the concatenation of dir/file.
    */
   static int Grep(const char* dir, const char* file, const char* expression);
   
   /**
-   * remove /cygdrive/d and replace with d:/
+   * Convert a path containing a cygwin drive specifier to its natural
+   * equivalent.
    */
   static void ConvertCygwinPath(std::string& pathname);
 
   /**
-   * Read a cmake function from an input file.  This
+   * Read a CMake rule (or function) from an input file.  This
    * returns the name of the function and a list of its 
    * arguments.
    */
   static bool ParseFunction(std::ifstream&, 
                             std::string& name,
                             std::vector<std::string>& arguments);
+
   /**
-   *  Extract space separated arguments from a string.
+   *  Extract white-space separated arguments from a string.
    *  Double quoted strings are accepted with spaces.
    *  This is called by ParseFunction.
    */
   static void GetArguments(std::string& line,
                            std::vector<std::string>& arguments);
+
   /**
    * Display an error message.
    */
diff --git a/Source/cmUnixMakefileGenerator.cxx b/Source/cmUnixMakefileGenerator.cxx
index 3363362..8037de9 100644
--- a/Source/cmUnixMakefileGenerator.cxx
+++ b/Source/cmUnixMakefileGenerator.cxx
@@ -1,3 +1,18 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
 #include "cmUnixMakefileGenerator.h"
 #include "cmMakefile.h"
 #include "cmStandardIncludes.h"
@@ -13,7 +28,6 @@ void cmUnixMakefileGenerator::GenerateMakefile()
   this->OutputMakefile("CMakeTargets.make"); 
 }
 
-
 // Output the depend information for all the classes 
 // in the makefile.  These would have been generated
 // by the class cmMakeDepend GenerateMakefile
diff --git a/Source/cmUnixMakefileGenerator.h b/Source/cmUnixMakefileGenerator.h
index 5f3d8f6..b941470 100644
--- a/Source/cmUnixMakefileGenerator.h
+++ b/Source/cmUnixMakefileGenerator.h
@@ -13,23 +13,33 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * itkUnixMakefile is used generate unix makefiles.
- */
-
 #ifndef cmUnixMakefileGenerator_h
 #define cmUnixMakefileGenerator_h
+
 #include "cmMakefile.h"
 #include "cmMakefileGenerator.h"
 
+/** \class cmUnixMakefileGenerator
+ * \brief Write a Unix makefiles.
+ *
+ * cmUnixMakefileGenerator produces a Unix makefile from its
+ * member m_Makefile.
+ */
 class cmUnixMakefileGenerator : public cmMakefileGenerator
 {
 public:
-  /** 
-   * Write the makefile to the named file
+  /**
+   * Produce the makefile (in this case a Unix makefile).
    */
   virtual void GenerateMakefile();
+
+  /**
+   * Output the depend information for all the classes 
+   * in the makefile.  These would have been generated
+   * by the class cmMakeDepend.
+   */
   void OutputDepends(std::ostream&);
+
 protected:
   void OutputMakefile(const char* file);
   void OutputDependLibraries(std::ostream&);
diff --git a/Source/cmWindowsConfigure.cxx b/Source/cmWindowsConfigure.cxx
index 17e46b2..fe81508 100644
--- a/Source/cmWindowsConfigure.cxx
+++ b/Source/cmWindowsConfigure.cxx
@@ -1,3 +1,18 @@
+/*=========================================================================
+
+  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.
+
+=========================================================================*/
 #include "cmWindowsConfigure.h"
 #include "cmStandardIncludes.h"
 #include "cmSystemTools.h"
diff --git a/Source/cmWindowsConfigure.h b/Source/cmWindowsConfigure.h
index 8922d97..191ee1d 100644
--- a/Source/cmWindowsConfigure.h
+++ b/Source/cmWindowsConfigure.h
@@ -13,34 +13,43 @@
   See COPYRIGHT.txt for copyright details.
 
 =========================================================================*/
-/**
- * cmWindowsConfigure : a class that configures the build
- * on windows where autoconf configure can not be used.
- * The system specific .h files normal generated by autoconf
- * should be generated by sub-classes of this class.
- */
 #ifndef cmWindowsConfigure_h
 #define cmWindowsConfigure_h
+
 #include "cmStandardIncludes.h"
 
+/** \class cmWindowsConfigure
+ * \brief Configure the build process on Windows systems.
+ * 
+ * cmWindowsConfigure configures the build process
+ * on windows where the Unix autoconf configure can not be used.
+ * The system specific .h files normally generated by autoconf
+ * should be generated by sub-classes of this class.
+ */
 class cmWindowsConfigure
 {
 public:
   /**
-   * Set the path to the top level of the source directory
+   * Set the path to the top level of the source directory.
    */
   void SetWhereSource(const char* dir) 
     {
-      m_WhereSource = dir;
+    m_WhereSource = dir;
     }
+
   /**
-   * Set the path to the top level of the build directory
+   * Set the path to the top level of the build directory.
    */
   void SetWhereBuild(const char* dir)
     {
       m_WhereBuild = dir;
     }
+
+  /**
+   * Perform the configure process.
+   */
   virtual bool Configure(const char* input);
+
 protected:
   std::string m_WhereSource;
   std::string m_WhereBuild;