diff --git a/Makefile b/Makefile
index 884f81d876e..a716d534af2 100644
--- a/Makefile
+++ b/Makefile
@@ -701,7 +701,7 @@ test/options.o: test/options.cpp test/options.h
 test/test64bit.o: test/test64bit.cpp lib/addoninfo.h lib/check.h lib/check64bit.h lib/checkers.h lib/color.h lib/config.h lib/errorlogger.h lib/errortypes.h lib/library.h lib/mathlib.h lib/path.h lib/platform.h lib/settings.h lib/standards.h lib/tokenize.h lib/tokenlist.h lib/utils.h test/fixture.h test/helpers.h
 	$(CXX) ${INCLUDE_FOR_TEST} $(CPPFLAGS) $(CXXFLAGS) -c -o $@ test/test64bit.cpp
 
-test/testanalyzerinformation.o: test/testanalyzerinformation.cpp lib/addoninfo.h lib/analyzerinfo.h lib/check.h lib/checkers.h lib/color.h lib/config.h lib/errorlogger.h lib/errortypes.h lib/library.h lib/mathlib.h lib/platform.h lib/settings.h lib/standards.h lib/utils.h test/fixture.h
+test/testanalyzerinformation.o: test/testanalyzerinformation.cpp lib/addoninfo.h lib/analyzerinfo.h lib/check.h lib/checkers.h lib/color.h lib/config.h lib/errorlogger.h lib/errortypes.h lib/filesettings.h lib/library.h lib/mathlib.h lib/path.h lib/platform.h lib/settings.h lib/standards.h lib/utils.h test/fixture.h
 	$(CXX) ${INCLUDE_FOR_TEST} $(CPPFLAGS) $(CXXFLAGS) -c -o $@ test/testanalyzerinformation.cpp
 
 test/testassert.o: test/testassert.cpp lib/addoninfo.h lib/check.h lib/checkassert.h lib/checkers.h lib/color.h lib/config.h lib/errorlogger.h lib/errortypes.h lib/library.h lib/mathlib.h lib/path.h lib/platform.h lib/settings.h lib/standards.h lib/tokenize.h lib/tokenlist.h lib/utils.h test/fixture.h test/helpers.h
diff --git a/gui/checkthread.cpp b/gui/checkthread.cpp
index 40396153b9c..e6fc23a0fd8 100644
--- a/gui/checkthread.cpp
+++ b/gui/checkthread.cpp
@@ -245,7 +245,7 @@ void CheckThread::runAddonsAndTools(const Settings& settings, const FileSettings
 
             const std::string &buildDir = settings.buildDir;
             if (!buildDir.empty()) {
-                analyzerInfoFile = QString::fromStdString(AnalyzerInformation::getAnalyzerInfoFile(buildDir, fileSettings->filename(), fileSettings->cfg));
+                analyzerInfoFile = QString::fromStdString(AnalyzerInformation::getAnalyzerInfoFile(buildDir, fileSettings->filename(), fileSettings->cfg, fileSettings->fileIndex));
 
                 QStringList args2(args);
                 args2.insert(0,"-E");
diff --git a/lib/analyzerinfo.cpp b/lib/analyzerinfo.cpp
index 9d5b914c2bd..dfb953c9445 100644
--- a/lib/analyzerinfo.cpp
+++ b/lib/analyzerinfo.cpp
@@ -25,6 +25,7 @@
 
 #include <cstring>
 #include <map>
+#include <sstream>
 
 #include "xml.h"
 
@@ -47,21 +48,30 @@ static std::string getFilename(const std::string &fullpath)
 
 void AnalyzerInformation::writeFilesTxt(const std::string &buildDir, const std::list<std::string> &sourcefiles, const std::string &userDefines, const std::list<FileSettings> &fileSettings)
 {
-    std::map<std::string, unsigned int> fileCount;
-
     const std::string filesTxt(buildDir + "/files.txt");
     std::ofstream fout(filesTxt);
+    fout << getFilesTxt(sourcefiles, userDefines, fileSettings);
+}
+
+std::string AnalyzerInformation::getFilesTxt(const std::list<std::string> &sourcefiles, const std::string &userDefines, const std::list<FileSettings> &fileSettings) {
+    std::ostringstream ret;
+
+    std::map<std::string, unsigned int> fileCount;
+
     for (const std::string &f : sourcefiles) {
         const std::string afile = getFilename(f);
-        fout << afile << ".a" << (++fileCount[afile]) << "::" << Path::simplifyPath(f) << '\n';
+        ret << afile << ".a" << (++fileCount[afile]) << sep << sep << sep << Path::simplifyPath(f) << '\n';
         if (!userDefines.empty())
-            fout << afile << ".a" << (++fileCount[afile]) << ":" << userDefines << ":" << Path::simplifyPath(f) << '\n';
+            ret << afile << ".a" << (++fileCount[afile]) << sep << userDefines << sep << sep << Path::simplifyPath(f) << '\n';
     }
 
     for (const FileSettings &fs : fileSettings) {
         const std::string afile = getFilename(fs.filename());
-        fout << afile << ".a" << (++fileCount[afile]) << ":" << fs.cfg << ":" << Path::simplifyPath(fs.filename()) << std::endl;
+        const std::string id = fs.fileIndex > 0 ? std::to_string(fs.fileIndex) : "";
+        ret << afile << ".a" << (++fileCount[afile]) << sep << fs.cfg << sep << id << sep << Path::simplifyPath(fs.filename()) << std::endl;
     }
+
+    return ret.str();
 }
 
 void AnalyzerInformation::close()
@@ -96,25 +106,26 @@ static bool skipAnalysis(const std::string &analyzerInfoFile, std::size_t hash,
     return true;
 }
 
-std::string AnalyzerInformation::getAnalyzerInfoFileFromFilesTxt(std::istream& filesTxt, const std::string &sourcefile, const std::string &cfg)
+std::string AnalyzerInformation::getAnalyzerInfoFileFromFilesTxt(std::istream& filesTxt, const std::string &sourcefile, const std::string &cfg, int fileIndex)
 {
+    const std::string id = (fileIndex > 0) ? std::to_string(fileIndex) : "";
     std::string line;
-    const std::string end(':' + cfg + ':' + Path::simplifyPath(sourcefile));
+    const std::string end(sep + cfg + sep + id + sep + Path::simplifyPath(sourcefile));
     while (std::getline(filesTxt,line)) {
         if (line.size() <= end.size() + 2U)
             continue;
         if (!endsWith(line, end.c_str(), end.size()))
             continue;
-        return line.substr(0,line.find(':'));
+        return line.substr(0,line.find(sep));
     }
     return "";
 }
 
-std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg)
+std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, int fileIndex)
 {
     std::ifstream fin(Path::join(buildDir, "files.txt"));
     if (fin.is_open()) {
-        const std::string& ret = getAnalyzerInfoFileFromFilesTxt(fin, sourcefile, cfg);
+        const std::string& ret = getAnalyzerInfoFileFromFilesTxt(fin, sourcefile, cfg, fileIndex);
         if (!ret.empty())
             return Path::join(buildDir, ret);
     }
@@ -128,13 +139,13 @@ std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir
     return Path::join(buildDir, filename) + ".analyzerinfo";
 }
 
-bool AnalyzerInformation::analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, std::size_t hash, std::list<ErrorMessage> &errors)
+bool AnalyzerInformation::analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, int fileIndex, std::size_t hash, std::list<ErrorMessage> &errors)
 {
     if (buildDir.empty() || sourcefile.empty())
         return true;
     close();
 
-    mAnalyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(buildDir,sourcefile,cfg);
+    mAnalyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(buildDir,sourcefile,cfg,fileIndex);
 
     if (skipAnalysis(mAnalyzerInfoFile, hash, errors))
         return false;
@@ -161,3 +172,31 @@ void AnalyzerInformation::setFileInfo(const std::string &check, const std::strin
     if (mOutputStream.is_open() && !fileInfo.empty())
         mOutputStream << "  <FileInfo check=\"" << check << "\">\n" << fileInfo << "  </FileInfo>\n";
 }
+
+bool AnalyzerInformation::Info::parse(const std::string& filesTxtLine) {
+    const std::string::size_type sep1 = filesTxtLine.find(sep);
+    if (sep1 == std::string::npos)
+        return false;
+    const std::string::size_type sep2 = filesTxtLine.find(sep, sep1+1);
+    if (sep2 == std::string::npos)
+        return false;
+    const std::string::size_type sep3 = filesTxtLine.find(sep, sep2+1);
+    if (sep3 == std::string::npos)
+        return false;
+
+    if (sep3 == sep2 + 1)
+        fileIndex = 0;
+    else {
+        try {
+            fileIndex = std::stoi(filesTxtLine.substr(sep2+1, sep3-sep2-1));
+        } catch (const std::exception&) {
+            return false;
+        }
+    }
+
+    afile = filesTxtLine.substr(0, sep1);
+    cfg = filesTxtLine.substr(sep1+1, sep2-sep1-1);
+    sourceFile = filesTxtLine.substr(sep3+1);
+    return true;
+}
+
diff --git a/lib/analyzerinfo.h b/lib/analyzerinfo.h
index 04f41ac4e99..e5466906707 100644
--- a/lib/analyzerinfo.h
+++ b/lib/analyzerinfo.h
@@ -51,16 +51,30 @@ class CPPCHECKLIB AnalyzerInformation {
 public:
     ~AnalyzerInformation();
 
+    static std::string getFilesTxt(const std::list<std::string> &sourcefiles, const std::string &userDefines, const std::list<FileSettings> &fileSettings);
+
     static void writeFilesTxt(const std::string &buildDir, const std::list<std::string> &sourcefiles, const std::string &userDefines, const std::list<FileSettings> &fileSettings);
 
     /** Close current TU.analyzerinfo file */
     void close();
-    bool analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, std::size_t hash, std::list<ErrorMessage> &errors);
+    bool analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, int fileIndex, std::size_t hash, std::list<ErrorMessage> &errors);
     void reportErr(const ErrorMessage &msg);
     void setFileInfo(const std::string &check, const std::string &fileInfo);
-    static std::string getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg);
+    static std::string getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, int fileIndex);
+
+    static const char sep = ':';
+
+    class CPPCHECKLIB Info {
+    public:
+        bool parse(const std::string& filesTxtLine);
+        std::string afile;
+        std::string cfg;
+        int fileIndex = 0;
+        std::string sourceFile;
+    };
+
 protected:
-    static std::string getAnalyzerInfoFileFromFilesTxt(std::istream& filesTxt, const std::string &sourcefile, const std::string &cfg);
+    static std::string getAnalyzerInfoFileFromFilesTxt(std::istream& filesTxt, const std::string &sourcefile, const std::string &cfg, int fileIndex);
 private:
     std::ofstream mOutputStream;
     std::string mAnalyzerInfoFile;
diff --git a/lib/cppcheck.cpp b/lib/cppcheck.cpp
index e079cf0354d..68a3bd93213 100644
--- a/lib/cppcheck.cpp
+++ b/lib/cppcheck.cpp
@@ -331,16 +331,16 @@ static std::vector<std::string> split(const std::string &str, const std::string
     return ret;
 }
 
-static std::string getDumpFileName(const Settings& settings, const std::string& filename)
+static std::string getDumpFileName(const Settings& settings, const std::string& filename, int fileIndex)
 {
-    std::string extension;
-    if (settings.dump || !settings.buildDir.empty())
-        extension = ".dump";
-    else
-        extension = "." + std::to_string(settings.pid) + ".dump";
+    std::string extension = ".dump";
+    if (fileIndex > 0)
+        extension = "." + std::to_string(fileIndex) + extension;
+    if (!settings.dump && settings.buildDir.empty())
+        extension = "." + std::to_string(settings.pid) + extension;
 
     if (!settings.dump && !settings.buildDir.empty())
-        return AnalyzerInformation::getAnalyzerInfoFile(settings.buildDir, filename, "") + extension;
+        return AnalyzerInformation::getAnalyzerInfoFile(settings.buildDir, filename, "", fileIndex) + extension;
     return filename + extension;
 }
 
@@ -351,12 +351,13 @@ static std::string getCtuInfoFileName(const std::string &dumpFile)
 
 static void createDumpFile(const Settings& settings,
                            const FileWithDetails& file,
+                           int fileIndex,
                            std::ofstream& fdump,
                            std::string& dumpFile)
 {
     if (!settings.dump && settings.addons.empty())
         return;
-    dumpFile = getDumpFileName(settings, file.spath());
+    dumpFile = getDumpFileName(settings, file.spath(), fileIndex);
 
     fdump.open(dumpFile);
     if (!fdump.is_open())
@@ -649,7 +650,7 @@ static std::string getClangFlags(const Settings& setting, Standards::Language la
 }
 
 // TODO: clear error list before returning
-unsigned int CppCheck::checkClang(const FileWithDetails &file)
+unsigned int CppCheck::checkClang(const FileWithDetails &file, int fileIndex)
 {
     // TODO: clear exitcode
 
@@ -662,7 +663,7 @@ unsigned int CppCheck::checkClang(const FileWithDetails &file)
     // TODO: get language from FileWithDetails object
     std::string clangStderr;
     if (!mSettings.buildDir.empty())
-        clangStderr = AnalyzerInformation::getAnalyzerInfoFile(mSettings.buildDir, file.spath(), "") + ".clang-stderr";
+        clangStderr = AnalyzerInformation::getAnalyzerInfoFile(mSettings.buildDir, file.spath(), "", fileIndex) + ".clang-stderr";
 
     std::string exe = mSettings.clangExecutable;
 #ifdef _WIN32
@@ -732,7 +733,7 @@ unsigned int CppCheck::checkClang(const FileWithDetails &file)
         // create dumpfile
         std::ofstream fdump;
         std::string dumpFile;
-        createDumpFile(mSettings, file, fdump, dumpFile);
+        createDumpFile(mSettings, file, fileIndex, fdump, dumpFile);
         if (fdump.is_open()) {
             fdump << getLibraryDumpData();
             // TODO: use tinyxml2 to create XML
@@ -776,9 +777,9 @@ unsigned int CppCheck::check(const FileWithDetails &file)
 
     unsigned int returnValue;
     if (mSettings.clang)
-        returnValue = checkClang(file);
+        returnValue = checkClang(file, 0);
     else
-        returnValue = checkFile(file, "");
+        returnValue = checkFile(file, "", 0);
 
     // TODO: call analyseClangTidy()
 
@@ -788,7 +789,7 @@ unsigned int CppCheck::check(const FileWithDetails &file)
 unsigned int CppCheck::check(const FileWithDetails &file, const std::string &content)
 {
     std::istringstream iss(content);
-    return checkFile(file, "", &iss);
+    return checkFile(file, "", 0, &iss);
 }
 
 unsigned int CppCheck::check(const FileSettings &fs)
@@ -824,7 +825,7 @@ unsigned int CppCheck::check(const FileSettings &fs)
     }
     // need to pass the externally provided ErrorLogger instead of our internal wrapper
     CppCheck temp(tempSettings, mSuppressions, mErrorLoggerDirect, mUseGlobalSuppressions, mExecuteCommand);
-    const unsigned int returnValue = temp.checkFile(fs.file, fs.cfg);
+    const unsigned int returnValue = temp.checkFile(fs.file, fs.cfg, fs.fileIndex);
     if (mUnusedFunctionsCheck)
         mUnusedFunctionsCheck->updateFunctionData(*temp.mUnusedFunctionsCheck);
     while (!temp.mFileInfo.empty()) {
@@ -861,7 +862,7 @@ static std::size_t calculateHash(const Preprocessor& preprocessor, const simplec
     return preprocessor.calculateHash(tokens, toolinfo.str());
 }
 
-unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string &cfgname, std::istream* fileStream)
+unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string &cfgname, int fileIndex, std::istream* fileStream)
 {
     // TODO: move to constructor when CppCheck no longer owns the settings
     if (mSettings.checks.isEnabled(Checks::unusedFunction) && !mUnusedFunctionsCheck)
@@ -938,7 +939,7 @@ unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string
                     mLogger->setAnalyzerInfo(nullptr);
 
                     std::list<ErrorMessage> errors;
-                    analyzerInformation->analyzeFile(mSettings.buildDir, file.spath(), cfgname, hash, errors);
+                    analyzerInformation->analyzeFile(mSettings.buildDir, file.spath(), cfgname, fileIndex, hash, errors);
                     analyzerInformation->setFileInfo("CheckUnusedFunctions", mUnusedFunctionsCheck->analyzerInfo(tokenizer));
                     analyzerInformation->close();
                 }
@@ -1012,7 +1013,7 @@ unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string
             // Calculate hash so it can be compared with old hash / future hashes
             const std::size_t hash = calculateHash(preprocessor, tokens1, mSettings, mSuppressions);
             std::list<ErrorMessage> errors;
-            if (!analyzerInformation->analyzeFile(mSettings.buildDir, file.spath(), cfgname, hash, errors)) {
+            if (!analyzerInformation->analyzeFile(mSettings.buildDir, file.spath(), cfgname, fileIndex, hash, errors)) {
                 while (!errors.empty()) {
                     mErrorLogger.reportErr(errors.front());
                     errors.pop_front();
@@ -1075,7 +1076,7 @@ unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string
         // write dump file xml prolog
         std::ofstream fdump;
         std::string dumpFile;
-        createDumpFile(mSettings, file, fdump, dumpFile);
+        createDumpFile(mSettings, file, fileIndex, fdump, dumpFile);
         if (fdump.is_open()) {
             fdump << getLibraryDumpData();
             fdump << dumpProlog;
@@ -1170,7 +1171,7 @@ unsigned int CppCheck::checkFile(const FileWithDetails& file, const std::string
 #endif
 
                     // Simplify tokens into normal form, skip rest of iteration if failed
-                    if (!tokenizer.simplifyTokens1(currentConfig))
+                    if (!tokenizer.simplifyTokens1(currentConfig, fileIndex))
                         continue;
 
                     // dump xml if --dump
@@ -1812,12 +1813,12 @@ void CppCheck::executeAddonsWholeProgram(const std::list<FileWithDetails> &files
 
     std::vector<std::string> ctuInfoFiles;
     for (const auto &f: files) {
-        const std::string &dumpFileName = getDumpFileName(mSettings, f.path());
+        const std::string &dumpFileName = getDumpFileName(mSettings, f.path(), 0);
         ctuInfoFiles.push_back(getCtuInfoFileName(dumpFileName));
     }
 
     for (const auto &f: fileSettings) {
-        const std::string &dumpFileName = getDumpFileName(mSettings, f.filename());
+        const std::string &dumpFileName = getDumpFileName(mSettings, f.filename(), f.fileIndex);
         ctuInfoFiles.push_back(getCtuInfoFileName(dumpFileName));
     }
 
@@ -1944,7 +1945,7 @@ void CppCheck::analyseClangTidy(const FileSettings &fileSettings)
     std::string line;
 
     if (!mSettings.buildDir.empty()) {
-        const std::string analyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(mSettings.buildDir, fileSettings.filename(), "");
+        const std::string analyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(mSettings.buildDir, fileSettings.filename(), "", fileSettings.fileIndex);
         std::ofstream fcmd(analyzerInfoFile + ".clang-tidy-cmd");
         fcmd << istr.str();
     }
@@ -2036,14 +2037,11 @@ unsigned int CppCheck::analyseWholeProgram(const std::string &buildDir, const st
     std::ifstream fin(filesTxt);
     std::string filesTxtLine;
     while (std::getline(fin, filesTxtLine)) {
-        const std::string::size_type firstColon = filesTxtLine.find(':');
-        if (firstColon == std::string::npos)
-            continue;
-        const std::string::size_type lastColon = filesTxtLine.rfind(':');
-        if (firstColon == lastColon)
+        AnalyzerInformation::Info filesTxtInfo;
+        if (!filesTxtInfo.parse(filesTxtLine))
             continue;
-        const std::string xmlfile = buildDir + '/' + filesTxtLine.substr(0,firstColon);
-        //const std::string sourcefile = filesTxtLine.substr(lastColon+1);
+
+        const std::string xmlfile = buildDir + '/' + filesTxtInfo.afile;
 
         tinyxml2::XMLDocument doc;
         const tinyxml2::XMLError error = doc.LoadFile(xmlfile.c_str());
@@ -2068,7 +2066,7 @@ unsigned int CppCheck::analyseWholeProgram(const std::string &buildDir, const st
             for (const Check *check : Check::instances()) {
                 if (checkClassAttr == check->name()) {
                     Check::FileInfo* fi = check->loadFileInfoFromXml(e);
-                    fi->file0 = filesTxtLine.substr(firstColon + 2);
+                    fi->file0 = filesTxtInfo.sourceFile;
                     fileInfoList.push_back(fi);
                 }
             }
diff --git a/lib/cppcheck.h b/lib/cppcheck.h
index 67acbf626b6..d7c326704a1 100644
--- a/lib/cppcheck.h
+++ b/lib/cppcheck.h
@@ -169,7 +169,7 @@ class CPPCHECKLIB CppCheck {
      * @param fileStream stream the file content can be read from
      * @return number of errors found
      */
-    unsigned int checkFile(const FileWithDetails& file, const std::string &cfgname, std::istream* fileStream = nullptr);
+    unsigned int checkFile(const FileWithDetails& file, const std::string &cfgname, int fileIndex, std::istream* fileStream = nullptr);
 
     /**
      * @brief Check normal tokens
@@ -198,7 +198,7 @@ class CPPCHECKLIB CppCheck {
     void executeRules(const std::string &tokenlist, const TokenList &list);
 #endif
 
-    unsigned int checkClang(const FileWithDetails &file);
+    unsigned int checkClang(const FileWithDetails &file, int fileIndex);
 
     const Settings& mSettings;
     Suppressions& mSuppressions;
diff --git a/lib/filesettings.h b/lib/filesettings.h
index 601aceea4f1..2c125264bbc 100644
--- a/lib/filesettings.h
+++ b/lib/filesettings.h
@@ -80,6 +80,7 @@ struct CPPCHECKLIB FileSettings {
         : file(std::move(path), lang, size)
     {}
 
+    int fileIndex = 0;
     std::string cfg;
     FileWithDetails file;
     const std::string& filename() const
diff --git a/lib/importproject.cpp b/lib/importproject.cpp
index fdcf5441db9..a4b183aca35 100644
--- a/lib/importproject.cpp
+++ b/lib/importproject.cpp
@@ -355,6 +355,8 @@ bool ImportProject::importCompileCommands(std::istream &istr)
         return false;
     }
 
+    std::map<std::string, int> fileIndex;
+
     for (const picojson::value &fileInfo : compileCommands.get<picojson::array>()) {
         picojson::object obj = fileInfo.get<picojson::object>();
         std::string dirpath = Path::fromNativeSeparators(obj["directory"].get<std::string>());
@@ -420,10 +422,13 @@ bool ImportProject::importCompileCommands(std::istream &istr)
             printError("'" + path + "' from compilation database does not exist");
             return false;
         }
-        FileSettings fs{std::move(path), Standards::Language::None, 0}; // file will be identified later on
+        FileSettings fs{path, Standards::Language::None, 0}; // file will be identified later on
         fsParseCommand(fs, command); // read settings; -D, -I, -U, -std, -m*, -f*
         std::map<std::string, std::string, cppcheck::stricmp> variables;
         fsSetIncludePaths(fs, directory, fs.includePaths, variables);
+        // Assign a unique index to each file path. If the file path already exists in the map,
+        // increment the index to handle duplicate file entries.
+        fs.fileIndex = fileIndex[path]++;
         fileSettings.push_back(std::move(fs));
     }
 
diff --git a/lib/summaries.cpp b/lib/summaries.cpp
index bcedbb9fc2b..9226094baec 100644
--- a/lib/summaries.cpp
+++ b/lib/summaries.cpp
@@ -34,7 +34,7 @@
 
 
 
-std::string Summaries::create(const Tokenizer &tokenizer, const std::string &cfg)
+std::string Summaries::create(const Tokenizer &tokenizer, const std::string &cfg, int fileIndex)
 {
     const SymbolDatabase *symbolDatabase = tokenizer.getSymbolDatabase();
     const Settings &settings = tokenizer.getSettings();
@@ -82,7 +82,7 @@ std::string Summaries::create(const Tokenizer &tokenizer, const std::string &cfg
     }
 
     if (!settings.buildDir.empty()) {
-        std::string filename = AnalyzerInformation::getAnalyzerInfoFile(settings.buildDir, tokenizer.list.getSourceFilePath(), cfg);
+        std::string filename = AnalyzerInformation::getAnalyzerInfoFile(settings.buildDir, tokenizer.list.getSourceFilePath(), cfg, fileIndex);
         const std::string::size_type pos = filename.rfind(".a");
         if (pos != std::string::npos) {
             filename[pos+1] = 's';
diff --git a/lib/summaries.h b/lib/summaries.h
index 87d3c5b5d63..238ea4107d3 100644
--- a/lib/summaries.h
+++ b/lib/summaries.h
@@ -29,7 +29,7 @@
 class Tokenizer;
 
 namespace Summaries {
-    CPPCHECKLIB std::string create(const Tokenizer &tokenizer, const std::string &cfg);
+    CPPCHECKLIB std::string create(const Tokenizer &tokenizer, const std::string &cfg, int fileIndex);
     CPPCHECKLIB void loadReturn(const std::string &buildDir, std::set<std::string> &summaryReturn);
 }
 
diff --git a/lib/tokenize.cpp b/lib/tokenize.cpp
index fa078eaf445..dc55ebe1409 100644
--- a/lib/tokenize.cpp
+++ b/lib/tokenize.cpp
@@ -3375,7 +3375,7 @@ void Tokenizer::simplifyUsingError(const Token* usingStart, const Token* usingEn
     }
 }
 
-bool Tokenizer::simplifyTokens1(const std::string &configuration)
+bool Tokenizer::simplifyTokens1(const std::string &configuration, int fileIndex)
 {
     // Fill the map mTypeSize..
     fillTypeSizes();
@@ -3408,7 +3408,7 @@ bool Tokenizer::simplifyTokens1(const std::string &configuration)
     });
 
     if (!mSettings.buildDir.empty())
-        Summaries::create(*this, configuration);
+        Summaries::create(*this, configuration, fileIndex);
 
     // TODO: apply this through Settings::ValueFlowOptions
     // TODO: do not run valueflow if no checks are being performed at all - e.g. unusedFunctions only
diff --git a/lib/tokenize.h b/lib/tokenize.h
index 0f0363354e9..7b927124deb 100644
--- a/lib/tokenize.h
+++ b/lib/tokenize.h
@@ -79,7 +79,7 @@ class CPPCHECKLIB Tokenizer {
      */
     bool isScopeNoReturn(const Token *endScopeToken, bool *unknown = nullptr) const;
 
-    bool simplifyTokens1(const std::string &configuration);
+    bool simplifyTokens1(const std::string &configuration, int fileIndex=0);
 
 private:
     /** Set variable id */
diff --git a/releasenotes.txt b/releasenotes.txt
index 78f2dfba2a2..c84fe6a0479 100644
--- a/releasenotes.txt
+++ b/releasenotes.txt
@@ -23,4 +23,5 @@ Other:
 - Updated TinyXML-2 to v11.0.0
 - The minimum supported Python version has been bumped to 3.7.
 - CMake will now unconditionally use Boost.Containers if available. If CMake option `USE_BOOST` is specified it will now bail out when it is not found.
+- Fix checking a project that contains several project file entries for the same file.
 -
diff --git a/test/cli/dumpfile_test.py b/test/cli/dumpfile_test.py
index 9593e2a1660..6e52b3cebcc 100644
--- a/test/cli/dumpfile_test.py
+++ b/test/cli/dumpfile_test.py
@@ -1,5 +1,6 @@
 # python -m pytest dumpfile_test.py
 
+import json
 import os
 import pathlib
 
@@ -92,4 +93,29 @@ def test_language_unk_force_c(tmp_path):
 
 
 def test_language_unk_force_cpp(tmp_path):
-    __test_language(tmp_path, 'src', force_lang='c++', exp_lang='cpp')
\ No newline at end of file
+    __test_language(tmp_path, 'src', force_lang='c++', exp_lang='cpp')
+
+
+def test_duplicate_file_entries(tmpdir):  #13333
+    test_file = str(tmpdir / 'test.c')
+    with open(test_file, 'wt') as f:
+        f.write('x=1;\n')
+
+    project_file = str(tmpdir / 'compile_commands.json')
+    with open(project_file, 'wt') as f:
+        f.write(json.dumps([{
+               "file": test_file,
+               "directory": str(tmpdir),
+               "command": "cc -c test.c"
+            },{
+               "file": test_file,
+               "directory": str(tmpdir),
+               "command": "cc -c test.c"
+            }]))
+
+    args = ['--project=compile_commands.json', '--dump']
+    _, _, _ = cppcheck(args, cwd=str(tmpdir))
+
+    assert os.path.isfile(test_file + '.dump')
+    assert os.path.isfile(test_file + '.1.dump')
+
diff --git a/test/testanalyzerinformation.cpp b/test/testanalyzerinformation.cpp
index 6727efb1fcd..f1d94d4af3c 100644
--- a/test/testanalyzerinformation.cpp
+++ b/test/testanalyzerinformation.cpp
@@ -18,6 +18,7 @@
 
 
 #include "analyzerinfo.h"
+#include "filesettings.h"
 #include "fixture.h"
 
 #include <sstream>
@@ -30,16 +31,69 @@ class TestAnalyzerInformation : public TestFixture, private AnalyzerInformation
 
     void run() override {
         TEST_CASE(getAnalyzerInfoFile);
+        TEST_CASE(duplicateFile);
+        TEST_CASE(filesTextDuplicateFile);
+        TEST_CASE(parse);
     }
 
     void getAnalyzerInfoFile() const {
-        constexpr char filesTxt[] = "file1.a4::file1.c\n";
+        constexpr char filesTxt[] = "file1.a4:::file1.c\n";
         std::istringstream f1(filesTxt);
-        ASSERT_EQUALS("file1.a4", getAnalyzerInfoFileFromFilesTxt(f1, "file1.c", ""));
+        ASSERT_EQUALS("file1.a4", getAnalyzerInfoFileFromFilesTxt(f1, "file1.c", "", 0));
         std::istringstream f2(filesTxt);
-        ASSERT_EQUALS("file1.a4", getAnalyzerInfoFileFromFilesTxt(f2, "./file1.c", ""));
-        ASSERT_EQUALS("builddir/file1.c.analyzerinfo", AnalyzerInformation::getAnalyzerInfoFile("builddir", "file1.c", ""));
-        ASSERT_EQUALS("builddir/file1.c.analyzerinfo", AnalyzerInformation::getAnalyzerInfoFile("builddir", "some/path/file1.c", ""));
+        ASSERT_EQUALS("file1.a4", getAnalyzerInfoFileFromFilesTxt(f2, "./file1.c", "", 0));
+        ASSERT_EQUALS("builddir/file1.c.analyzerinfo", AnalyzerInformation::getAnalyzerInfoFile("builddir", "file1.c", "", 0));
+        ASSERT_EQUALS("builddir/file1.c.analyzerinfo", AnalyzerInformation::getAnalyzerInfoFile("builddir", "some/path/file1.c", "", 0));
+    }
+
+    void filesTextDuplicateFile() const {
+        std::list<FileSettings> fileSettings;
+        fileSettings.emplace_back("a.c", Standards::Language::C, 10);
+        fileSettings.back().fileIndex = 0;
+        fileSettings.emplace_back("a.c", Standards::Language::C, 10);
+        fileSettings.back().fileIndex = 1;
+
+        const char expected[] = "a.a1:::a.c\n"
+                                "a.a2::1:a.c\n";
+
+        ASSERT_EQUALS(expected, getFilesTxt({}, "", fileSettings));
+    }
+
+    void duplicateFile() const {
+        // same file duplicated
+        constexpr char filesTxt[] = "file1.a1::1:file1.c\n"
+                                    "file1.a2::2:file1.c\n";
+        std::istringstream f1(filesTxt);
+        ASSERT_EQUALS("file1.a1", getAnalyzerInfoFileFromFilesTxt(f1, "file1.c", "", 1));
+        std::istringstream f2(filesTxt);
+        ASSERT_EQUALS("file1.a2", getAnalyzerInfoFileFromFilesTxt(f2, "file1.c", "", 2));
+    }
+
+    void parse() const {
+        AnalyzerInformation::Info info;
+
+        ASSERT_EQUALS(false, info.parse("a"));
+        ASSERT_EQUALS(false, info.parse("a:b"));
+        ASSERT_EQUALS(false, info.parse("a:b:c"));
+        ASSERT_EQUALS(false, info.parse("a:b:c:d"));
+
+        ASSERT_EQUALS(true, info.parse("a:b::d"));
+        ASSERT_EQUALS("a", info.afile);
+        ASSERT_EQUALS("b", info.cfg);
+        ASSERT_EQUALS(0, info.fileIndex);
+        ASSERT_EQUALS("d", info.sourceFile);
+
+        ASSERT_EQUALS(true, info.parse("e:f:12:g"));
+        ASSERT_EQUALS("e", info.afile);
+        ASSERT_EQUALS("f", info.cfg);
+        ASSERT_EQUALS(12, info.fileIndex);
+        ASSERT_EQUALS("g", info.sourceFile);
+
+        ASSERT_EQUALS(true, info.parse("odr1.a1:::C:/dm/cppcheck-fix-13333/test/cli/whole-program/odr1.cpp"));
+        ASSERT_EQUALS("odr1.a1", info.afile);
+        ASSERT_EQUALS("", info.cfg);
+        ASSERT_EQUALS(0, info.fileIndex);
+        ASSERT_EQUALS("C:/dm/cppcheck-fix-13333/test/cli/whole-program/odr1.cpp", info.sourceFile);
     }
 };
 
diff --git a/test/testimportproject.cpp b/test/testimportproject.cpp
index ca84d13cf44..42888a8e401 100644
--- a/test/testimportproject.cpp
+++ b/test/testimportproject.cpp
@@ -64,6 +64,7 @@ class TestImportProject : public TestFixture {
         TEST_CASE(importCompileCommands10); // #10887: include path with space
         TEST_CASE(importCompileCommands11); // include path order
         TEST_CASE(importCompileCommands12); // #13040: "directory" is parent directory, relative include paths
+        TEST_CASE(importCompileCommands13); // #13333: duplicate file entries
         TEST_CASE(importCompileCommandsArgumentsSection); // Handle arguments section
         TEST_CASE(importCompileCommandsNoCommandSection); // gracefully handles malformed json
         TEST_CASE(importCppcheckGuiProject);
@@ -338,6 +339,28 @@ class TestImportProject : public TestFixture {
         ASSERT_EQUALS("/x/", fs.includePaths.front());
     }
 
+    void importCompileCommands13() const { // #13333
+        REDIRECT;
+        constexpr char json[] =
+            R"([{
+               "file": "/x/src/1.c" ,
+               "directory": "/x",
+               "command": "cc -c -I. src/1.c"
+            },{
+               "file": "/x/src/1.c" ,
+               "directory": "/x",
+               "command": "cc -c -I. src/1.c"
+            }])";
+        std::istringstream istr(json);
+        TestImporter importer;
+        ASSERT_EQUALS(true, importer.importCompileCommands(istr));
+        ASSERT_EQUALS(2, importer.fileSettings.size());
+        const FileSettings &fs1 = importer.fileSettings.front();
+        const FileSettings &fs2 = importer.fileSettings.back();
+        ASSERT_EQUALS(0, fs1.fileIndex);
+        ASSERT_EQUALS(1, fs2.fileIndex);
+    }
+
     void importCompileCommandsArgumentsSection() const {
         REDIRECT;
         constexpr char json[] = "[ { \"directory\": \"/tmp/\","
diff --git a/test/testsummaries.cpp b/test/testsummaries.cpp
index 83674a4da8e..7896ffeb750 100644
--- a/test/testsummaries.cpp
+++ b/test/testsummaries.cpp
@@ -41,7 +41,7 @@ class TestSummaries : public TestFixture {
         // tokenize..
         SimpleTokenizer tokenizer(settingsDefault, *this);
         ASSERT_LOC(tokenizer.tokenize(code), file, line);
-        return Summaries::create(tokenizer, "");
+        return Summaries::create(tokenizer, "", 0);
     }
 
     void createSummaries1() {