diff --git a/src/plugins/clangtools/clangtidyclazytool.cpp b/src/plugins/clangtools/clangtidyclazytool.cpp
index f07fdcd3f73..ec743c97949 100644
--- a/src/plugins/clangtools/clangtidyclazytool.cpp
+++ b/src/plugins/clangtools/clangtidyclazytool.cpp
@@ -464,11 +464,11 @@ void ClangTidyClazyTool::handleStateUpdate()
 }
 
 QList<Diagnostic> ClangTidyClazyTool::read(const QString &filePath,
-                                           const Utils::FilePath &projectRootDir,
+                                           const QSet<Utils::FilePath> &projectFiles,
                                            const QString &logFilePath,
                                            QString *errorMessage) const
 {
-    return readSerializedDiagnostics(filePath, projectRootDir, logFilePath, errorMessage);
+    return readSerializedDiagnostics(filePath, projectFiles, logFilePath, errorMessage);
 }
 
 void ClangTidyClazyTool::onNewDiagnosticsAvailable(const QList<Diagnostic> &diagnostics)
diff --git a/src/plugins/clangtools/clangtidyclazytool.h b/src/plugins/clangtools/clangtidyclazytool.h
index c0765dc6a9e..17832905389 100644
--- a/src/plugins/clangtools/clangtidyclazytool.h
+++ b/src/plugins/clangtools/clangtidyclazytool.h
@@ -54,7 +54,7 @@ public:
     void startTool(bool askUserForFileSelection) final;
 
     QList<Diagnostic> read(const QString &filePath,
-                           const Utils::FilePath &projectRootDir,
+                           const QSet<Utils::FilePath> &projectFiles,
                            const QString &logFilePath,
                            QString *errorMessage) const final;
 
diff --git a/src/plugins/clangtools/clangtool.h b/src/plugins/clangtools/clangtool.h
index 0f322feb47b..1d94719759c 100644
--- a/src/plugins/clangtools/clangtool.h
+++ b/src/plugins/clangtools/clangtool.h
@@ -50,7 +50,7 @@ public:
     virtual void startTool(bool askUserForFileSelection) = 0;
 
     virtual QList<Diagnostic> read(const QString &filePath,
-                                   const Utils::FilePath &projectRootDir,
+                                   const QSet<Utils::FilePath> &projectFiles,
                                    const QString &logFilePath,
                                    QString *errorMessage) const = 0;
 
diff --git a/src/plugins/clangtools/clangtoolruncontrol.cpp b/src/plugins/clangtools/clangtoolruncontrol.cpp
index cc8dd249714..64672934172 100644
--- a/src/plugins/clangtools/clangtoolruncontrol.cpp
+++ b/src/plugins/clangtools/clangtoolruncontrol.cpp
@@ -288,6 +288,7 @@ void ClangToolRunControl::start()
     }
 
     m_projectInfo = CppTools::CppModelManager::instance()->projectInfo(m_target->project());
+    m_projectFiles = Utils::toSet(m_target->project()->files(Project::AllFiles));
 
     // Some projects provides CompilerCallData once a build is finished,
     if (m_projectInfo.configurationOrFilesChanged(m_projectInfoBeforeBuild)) {
@@ -360,6 +361,7 @@ void ClangToolRunControl::stop()
         QObject::disconnect(runner, nullptr, this, nullptr);
         delete runner;
     }
+    m_projectFiles.clear();
     m_runners.clear();
     m_unitsToProcess.clear();
     m_progress.reportFinished();
@@ -390,22 +392,14 @@ void ClangToolRunControl::analyzeNextFile()
                   Utils::StdOutFormat);
 }
 
-static Utils::FilePath cleanPath(const Utils::FilePath &filePath)
-{
-    return Utils::FilePath::fromString(QDir::cleanPath(filePath.toString()));
-}
-
 void ClangToolRunControl::onRunnerFinishedWithSuccess(const QString &filePath)
 {
     const QString logFilePath = qobject_cast<ClangToolRunner *>(sender())->logFilePath();
     qCDebug(LOG) << "onRunnerFinishedWithSuccess:" << logFilePath;
 
-    QTC_ASSERT(m_projectInfo.project(), return);
-    const Utils::FilePath projectRootDir = cleanPath(m_projectInfo.project()->projectDirectory());
-
     QString errorMessage;
     const QList<Diagnostic> diagnostics = tool()->read(filePath,
-                                                       projectRootDir,
+                                                       m_projectFiles,
                                                        logFilePath,
                                                        &errorMessage);
     QFile::remove(logFilePath); // Clean-up.
diff --git a/src/plugins/clangtools/clangtoolruncontrol.h b/src/plugins/clangtools/clangtoolruncontrol.h
index 92ecb5e2b23..2027d9513b1 100644
--- a/src/plugins/clangtools/clangtoolruncontrol.h
+++ b/src/plugins/clangtools/clangtoolruncontrol.h
@@ -104,6 +104,7 @@ private:
 
     QFutureInterface<void> m_progress;
     AnalyzeUnits m_unitsToProcess;
+    QSet<Utils::FilePath> m_projectFiles;
     QSet<ClangToolRunner *> m_runners;
     int m_initialFilesToProcessSize = 0;
     int m_filesAnalyzed = 0;
diff --git a/src/plugins/clangtools/clangtoolslogfilereader.cpp b/src/plugins/clangtools/clangtoolslogfilereader.cpp
index 63751181ee8..76c38f44bec 100644
--- a/src/plugins/clangtools/clangtoolslogfilereader.cpp
+++ b/src/plugins/clangtools/clangtoolslogfilereader.cpp
@@ -122,7 +122,7 @@ static ExplainingStep buildFixIt(const CXDiagnostic cxDiagnostic, unsigned index
 }
 
 static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic,
-                                  const Utils::FilePath &projectRootDir,
+                                  const QSet<Utils::FilePath> &projectFiles,
                                   const QString &nativeFilePath)
 {
     Diagnostic diagnostic;
@@ -136,7 +136,7 @@ static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic,
 
     diagnostic.location = diagLocationFromSourceLocation(cxLocation);
     const auto diagnosticFilePath = Utils::FilePath::fromString(diagnostic.location.filePath);
-    if (!diagnosticFilePath.isChildOf(projectRootDir))
+    if (!projectFiles.contains(diagnosticFilePath))
         return diagnostic;
 
     // TODO: Introduce CppTools::ProjectFile::isGenerated to filter these out properly
@@ -183,7 +183,7 @@ static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic,
 }
 
 static QList<Diagnostic> readSerializedDiagnostics_helper(const QString &filePath,
-                                                          const Utils::FilePath &projectRootDir,
+                                                          const QSet<Utils::FilePath> &projectFiles,
                                                           const QString &logFilePath)
 {
     QList<Diagnostic> list;
@@ -206,7 +206,7 @@ static QList<Diagnostic> readSerializedDiagnostics_helper(const QString &filePat
         Utils::ExecuteOnDestruction cleanUpDiagnostic([&]() {
             clang_disposeDiagnostic(cxDiagnostic);
         });
-        const Diagnostic diagnostic = buildDiagnostic(cxDiagnostic, projectRootDir, nativeFilePath);
+        const Diagnostic diagnostic = buildDiagnostic(cxDiagnostic, projectFiles, nativeFilePath);
         if (!diagnostic.isValid())
             continue;
 
@@ -232,14 +232,14 @@ static bool checkFilePath(const QString &filePath, QString *errorMessage)
 }
 
 QList<Diagnostic> readSerializedDiagnostics(const QString &filePath,
-                                            const Utils::FilePath &projectRootDir,
+                                            const QSet<Utils::FilePath> &projectFiles,
                                             const QString &logFilePath,
                                             QString *errorMessage)
 {
     if (!checkFilePath(logFilePath, errorMessage))
         return QList<Diagnostic>();
 
-    return readSerializedDiagnostics_helper(filePath, projectRootDir, logFilePath);
+    return readSerializedDiagnostics_helper(filePath, projectFiles, logFilePath);
 }
 
 } // namespace Internal
diff --git a/src/plugins/clangtools/clangtoolslogfilereader.h b/src/plugins/clangtools/clangtoolslogfilereader.h
index c95ce645ae9..de37c362b58 100644
--- a/src/plugins/clangtools/clangtoolslogfilereader.h
+++ b/src/plugins/clangtools/clangtoolslogfilereader.h
@@ -35,7 +35,7 @@ namespace ClangTools {
 namespace Internal {
 
 QList<Diagnostic> readSerializedDiagnostics(const QString &filePath,
-                                            const Utils::FilePath &projectRootDir,
+                                            const QSet<Utils::FilePath> &projectFiles,
                                             const QString &logFilePath,
                                             QString *errorMessage);