5 files changed, 61 insertions, 23 deletions
diff --git a/Source/cmDependsFortran.cxx b/Source/cmDependsFortran.cxx
index d5472a1..e4a146c 100644
--- a/Source/cmDependsFortran.cxx
+++ b/Source/cmDependsFortran.cxx
@@ -765,7 +765,11 @@ bool cmDependsFortran::ModulesDiffer(const char* modFile,
                                      const char* compilerId)
 {
   /*
-  gnu:
+  gnu >= 4.9:
+    A mod file is an ascii file compressed with gzip.
+    Compiling twice produces identical modules.
+
+  gnu < 4.9:
     A mod file is an ascii file.
     <bar.mod>
     FORTRAN module created from /path/to/foo.f90 on Sun Dec 30 22:47:58 2007
@@ -821,21 +825,30 @@ bool cmDependsFortran::ModulesDiffer(const char* modFile,
    */
   if (strcmp(compilerId, "GNU") == 0 )
     {
-    const char seq[1] = {'\n'};
-    const int seqlen = 1;
-
-    if(!cmDependsFortranStreamContainsSequence(finModFile, seq, seqlen))
+    // GNU Fortran 4.9 and later compress .mod files with gzip
+    // but also do not include a date so we can fall through to
+    // compare them without skipping any prefix.
+    unsigned char hdr[2];
+    bool okay = finModFile.read(reinterpret_cast<char*>(hdr), 2)? true:false;
+    finModFile.seekg(0);
+    if(!(okay && hdr[0] == 0x1f && hdr[1] == 0x8b))
       {
-      // The module is of unexpected format.  Assume it is different.
-      std::cerr << compilerId << " fortran module " << modFile
-                << " has unexpected format." << std::endl;
-      return true;
-      }
+      const char seq[1] = {'\n'};
+      const int seqlen = 1;
 
-    if(!cmDependsFortranStreamContainsSequence(finStampFile, seq, seqlen))
-      {
-      // The stamp must differ if the sequence is not contained.
-      return true;
+      if(!cmDependsFortranStreamContainsSequence(finModFile, seq, seqlen))
+        {
+        // The module is of unexpected format.  Assume it is different.
+        std::cerr << compilerId << " fortran module " << modFile
+                  << " has unexpected format." << std::endl;
+        return true;
+        }
+
+      if(!cmDependsFortranStreamContainsSequence(finStampFile, seq, seqlen))
+        {
+        // The stamp must differ if the sequence is not contained.
+        return true;
+        }
       }
     }
   else if(strcmp(compilerId, "Intel") == 0)
diff --git a/Source/cmGlobalNinjaGenerator.cxx b/Source/cmGlobalNinjaGenerator.cxx
index 731bc00..60643ac 100644
--- a/Source/cmGlobalNinjaGenerator.cxx
+++ b/Source/cmGlobalNinjaGenerator.cxx
@@ -972,7 +972,16 @@ void cmGlobalNinjaGenerator::WriteUnknownExplicitDependencies(std::ostream& os)
       {
       knownDependencies.insert( ng->ConvertToNinjaPath( j->c_str() ) );
       }
+    //get list files which are implicit dependencies as well and will be phony
+    //for rebuild manifest
+    std::vector<std::string> const& lf = (*i)->GetMakefile()->GetListFiles();
+    typedef std::vector<std::string>::const_iterator vect_it;
+    for(vect_it j = lf.begin(); j != lf.end(); ++j)
+      {
+      knownDependencies.insert( ng->ConvertToNinjaPath( j->c_str() ) );
+      }
     }
+  knownDependencies.insert( "CMakeCache.txt" );
 
   for(std::vector<cmGeneratorExpressionEvaluationFile*>::const_iterator
       li = this->EvaluationFiles.begin();
diff --git a/Source/cmSystemTools.cxx b/Source/cmSystemTools.cxx
index c7acfd0..575b973 100644
--- a/Source/cmSystemTools.cxx
+++ b/Source/cmSystemTools.cxx
@@ -2163,6 +2163,11 @@ void cmSystemTools::FindCMakeResources(const char* argv0)
   cmSystemToolsCMakeCommand = exe_dir;
   cmSystemToolsCMakeCommand += "/cmake";
   cmSystemToolsCMakeCommand += cmSystemTools::GetExecutableExtension();
+#ifndef CMAKE_BUILD_WITH_CMAKE
+  // The bootstrap cmake does not provide the other tools,
+  // so use the directory where they are about to be built.
+  exe_dir = CMAKE_BOOTSTRAP_BINARY_DIR "/bin";
+#endif
   cmSystemToolsCTestCommand = exe_dir;
   cmSystemToolsCTestCommand += "/ctest";
   cmSystemToolsCTestCommand += cmSystemTools::GetExecutableExtension();
@@ -2215,7 +2220,7 @@ void cmSystemTools::FindCMakeResources(const char* argv0)
     }
 #else
   // Bootstrap build knows its source.
-  cmSystemToolsCMakeRoot = CMAKE_ROOT_DIR;
+  cmSystemToolsCMakeRoot = CMAKE_BOOTSTRAP_SOURCE_DIR;
 #endif
 }
 
diff --git a/Source/cmake.cxx b/Source/cmake.cxx
index 7cbc1da..fafcca8 100644
--- a/Source/cmake.cxx
+++ b/Source/cmake.cxx
@@ -339,16 +339,24 @@ bool cmake::SetCacheArgs(const std::vector<std::string>& args)
         // The value is transformed if it is a filepath for example, so
         // we can't compare whether the value is already in the cache until
         // after we call AddCacheEntry.
-        const char *cachedValue =
-                              this->CacheManager->GetCacheValue(var.c_str());
+        bool haveValue = false;
+        std::string cachedValue;
+        if(this->WarnUnusedCli)
+          {
+          if(const char *v = this->CacheManager->GetCacheValue(var.c_str()))
+            {
+            haveValue = true;
+            cachedValue = v;
+            }
+          }
 
         this->CacheManager->AddCacheEntry(var.c_str(), value.c_str(),
           "No help, variable specified on the command line.", type);
+
         if(this->WarnUnusedCli)
           {
-          if (!cachedValue
-              || strcmp(this->CacheManager->GetCacheValue(var.c_str()),
-                        cachedValue) != 0)
+          if (!haveValue ||
+              cachedValue != this->CacheManager->GetCacheValue(var.c_str()))
             {
             this->WatchUnusedCli(var.c_str());
             }
diff --git a/bootstrap b/bootstrap
index 45f67cf..da84040 100755
--- a/bootstrap
+++ b/bootstrap
@@ -1474,9 +1474,11 @@ fi
 # When bootstrapping on MinGW with MSYS we must convert the source
 # directory to a windows path.
 if ${cmake_system_mingw}; then
-    cmake_root_dir=`cd "${cmake_source_dir}"; pwd -W`
+    CMAKE_BOOTSTRAP_SOURCE_DIR=`cd "${cmake_source_dir}"; pwd -W`
+    CMAKE_BOOTSTRAP_BINARY_DIR=`cd "${cmake_binary_dir}"; pwd -W`
 else
-    cmake_root_dir="${cmake_source_dir}"
+    CMAKE_BOOTSTRAP_SOURCE_DIR="${cmake_source_dir}"
+    CMAKE_BOOTSTRAP_BINARY_DIR="${cmake_binary_dir}"
 fi
 
 # Write CMake version
@@ -1484,7 +1486,8 @@ cmake_report cmVersionConfig.h${_tmp} "#define CMake_VERSION_MAJOR ${cmake_versi
 cmake_report cmVersionConfig.h${_tmp} "#define CMake_VERSION_MINOR ${cmake_version_minor}"
 cmake_report cmVersionConfig.h${_tmp} "#define CMake_VERSION_PATCH ${cmake_version_patch}"
 cmake_report cmVersionConfig.h${_tmp} "#define CMake_VERSION \"${cmake_version}\""
-cmake_report cmConfigure.h${_tmp} "#define CMAKE_ROOT_DIR \"${cmake_root_dir}\""
+cmake_report cmConfigure.h${_tmp} "#define CMAKE_BOOTSTRAP_SOURCE_DIR \"${CMAKE_BOOTSTRAP_SOURCE_DIR}\""
+cmake_report cmConfigure.h${_tmp} "#define CMAKE_BOOTSTRAP_BINARY_DIR \"${CMAKE_BOOTSTRAP_BINARY_DIR}\""
 cmake_report cmConfigure.h${_tmp} "#define CMAKE_DATA_DIR \"/bootstrap-not-insalled\""
 cmake_report cmConfigure.h${_tmp} "#define CMAKE_BOOTSTRAP"