Actually custom command can write wherever it wants to, such as temporary
folder or source folder, possibly violating rules that only build folder should
be affected. Therefore we should consider custom command dependency at any path
as possible side effect adding phony rule.
---
 Source/cmGlobalNinjaGenerator.cxx | 22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/Source/cmGlobalNinjaGenerator.cxx 
b/Source/cmGlobalNinjaGenerator.cxx
index eb01654..09ee128 100644
--- a/Source/cmGlobalNinjaGenerator.cxx
+++ b/Source/cmGlobalNinjaGenerator.cxx
@@ -1033,27 +1033,17 @@ void 
cmGlobalNinjaGenerator::WriteUnknownExplicitDependencies(std::ostream& os)
                       std::back_inserter(unkownExplicitDepends));
 
 
-  std::string const rootBuildDirectory =
-      this->GetCMakeInstance()->GetHomeOutputDirectory();
   for (std::vector<std::string>::const_iterator
        i = unkownExplicitDepends.begin();
        i != unkownExplicitDepends.end();
        ++i)
     {
-    //verify the file is in the build directory
-    std::string const absDepPath = cmSystemTools::CollapseFullPath(
-                                     i->c_str(), rootBuildDirectory.c_str());
-    bool const inBuildDir = cmSystemTools::IsSubDirectory(absDepPath.c_str(),
-                                                  rootBuildDirectory.c_str());
-    if(inBuildDir)
-      {
-      cmNinjaDeps deps(1,*i);
-      this->WritePhonyBuild(os,
-                            "",
-                            deps,
-                            deps);
-      }
-   }
+    cmNinjaDeps deps(1,*i);
+    this->WritePhonyBuild(os,
+                          "",
+                          deps,
+                          deps);
+    }
 }
 
 void cmGlobalNinjaGenerator::WriteBuiltinTargets(std::ostream& os)
-- 
1.9.3 (Apple Git-50)

-- 

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