diff --git a/cli/cppcheckexecutor.cpp b/cli/cppcheckexecutor.cpp
index b8742b687..e2c645161 100644
--- a/cli/cppcheckexecutor.cpp
+++ b/cli/cppcheckexecutor.cpp
@@ -17,6 +17,7 @@
  */
 
 #include "cppcheckexecutor.h"
+#include "analyzerinfo.h"
 #include "cmdlineparser.h"
 #include "cppcheck.h"
 #include "filelister.h"
@@ -803,11 +804,10 @@ int CppCheckExecutor::check_internal(CppCheck& cppcheck, int /*argc*/, const cha
     }
 
     if (!settings.buildDir.empty()) {
-        const std::string filename(settings.buildDir + "/files.txt");
-        std::ofstream fout(filename.c_str());
-        for (std::map<std::string, std::size_t>::const_iterator f = _files.begin(); f != _files.end(); ++f) {
-            fout << f->first << '\n';
-        }
+        std::list<std::string> fileNames;
+        for (std::map<std::string, std::size_t>::const_iterator i = _files.begin(); i != _files.end(); ++i)
+            fileNames.push_back(i->first);
+        AnalyzerInformation::writeFilesTxt(settings.buildDir, fileNames, settings.project.fileSettings);
     }
 
     unsigned int returnValue = 0;
diff --git a/lib/analyzerinfo.cpp b/lib/analyzerinfo.cpp
index 8c7027244..483e9a656 100644
--- a/lib/analyzerinfo.cpp
+++ b/lib/analyzerinfo.cpp
@@ -26,6 +26,39 @@ AnalyzerInformation::~AnalyzerInformation()
     close();
 }
 
+static std::string getFilename(const std::string &fullpath) {
+    std::string afile(fullpath);
+    std::string::size_type pos1 = fullpath.find_last_of("/\\");
+    pos1 = (pos1 == std::string::npos) ? 0U : (pos1 + 1U);
+    std::string::size_type pos2 = fullpath.rfind('.');
+    if (pos2 < pos1)
+        pos2 = std::string::npos;
+    if (pos2 != std::string::npos)
+        pos2 = pos2 - pos1;
+    return fullpath.substr(pos1,pos2);
+}
+
+void AnalyzerInformation::writeFilesTxt(const std::string &buildDir, const std::list<std::string> &sourcefiles, const std::list<ImportProject::FileSettings> &fileSettings)
+{
+    std::map<std::string, unsigned int> fileCount;
+
+    const std::string filesTxt(buildDir + "/files.txt");
+    std::ofstream fout(filesTxt.c_str());
+    for (std::list<std::string>::const_iterator f = sourcefiles.begin(); f != sourcefiles.end(); ++f) {
+        const std::string afile = getFilename(*f);
+        if (fileCount.find(afile) == fileCount.end())
+            fileCount[afile] = 0;
+        fout << afile << ".a" << (++fileCount[afile]) << "::" << Path::fromNativeSeparators(*f) << '\n';
+    }
+
+    for (std::list<ImportProject::FileSettings>::const_iterator fs = fileSettings.begin(); fs != fileSettings.end(); ++fs) {
+        const std::string afile = getFilename(fs->filename);
+        if (fileCount.find(afile) == fileCount.end())
+            fileCount[afile] = 0;
+        fout << afile << ".a" << (++fileCount[afile]) << ":" << fs->cfg << ":" << Path::fromNativeSeparators(fs->filename) << std::endl;
+    }
+}
+
 void AnalyzerInformation::close()
 {
     analyzerInfoFile.clear();
@@ -58,20 +91,21 @@ static bool skipAnalysis(const std::string &analyzerInfoFile, unsigned long long
     return true;
 }
 
-std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile)
+std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg)
 {
     const std::string files(buildDir + "/files.txt");
     std::ifstream fin(files.c_str());
     if (fin.is_open()) {
-        int id = 1;
         std::string line;
+        const std::string endsWith(':' + cfg + ':' + sourcefile);
         while (std::getline(fin,line)) {
-            if (line == sourcefile) {
-                std::ostringstream ostr;
-                ostr << buildDir << '/' << id << ".analyzeinfo";
-                return ostr.str();
-            }
-            id++;
+            if (line.size() <= endsWith.size() + 2U)
+                continue;
+            if (line.compare(line.size()-endsWith.size(), endsWith.size(), endsWith) != 0)
+                continue;
+            std::ostringstream ostr;
+            ostr << buildDir << '/' << line.substr(0,line.find(':'));
+            return ostr.str();
         }
     }
 
@@ -87,13 +121,13 @@ std::string AnalyzerInformation::getAnalyzerInfoFile(const std::string &buildDir
     return filename;
 }
 
-bool AnalyzerInformation::analyzeFile(const std::string &buildDir, const std::string &sourcefile, unsigned long long checksum, std::list<ErrorLogger::ErrorMessage> *errors)
+bool AnalyzerInformation::analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, unsigned long long checksum, std::list<ErrorLogger::ErrorMessage> *errors)
 {
     if (buildDir.empty() || sourcefile.empty())
         return true;
     close();
 
-    analyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(buildDir,sourcefile);
+    analyzerInfoFile = AnalyzerInformation::getAnalyzerInfoFile(buildDir,sourcefile,cfg);
 
     if (skipAnalysis(analyzerInfoFile, checksum, errors))
         return false;
diff --git a/lib/analyzerinfo.h b/lib/analyzerinfo.h
index d50054c4d..b1f365293 100644
--- a/lib/analyzerinfo.h
+++ b/lib/analyzerinfo.h
@@ -23,6 +23,8 @@
 
 #include "config.h"
 #include "errorlogger.h"
+#include "importproject.h"
+#include <list>
 #include <string>
 #include <fstream>
 
@@ -47,12 +49,14 @@ class CPPCHECKLIB AnalyzerInformation {
 public:
     ~AnalyzerInformation();
 
+    static void writeFilesTxt(const std::string &buildDir, const std::list<std::string> &sourcefiles, const std::list<ImportProject::FileSettings> &fileSettings);
+
     /** Close current TU.analyzerinfo file */
     void close();
-    bool analyzeFile(const std::string &buildDir, const std::string &sourcefile, unsigned long long checksum, std::list<ErrorLogger::ErrorMessage> *errors);
+    bool analyzeFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg, unsigned long long checksum, std::list<ErrorLogger::ErrorMessage> *errors);
     void reportErr(const ErrorLogger::ErrorMessage &msg, bool verbose);
     void setFileInfo(const std::string &check, const std::string &fileInfo);
-    static std::string getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile);
+    static std::string getAnalyzerInfoFile(const std::string &buildDir, const std::string &sourcefile, const std::string &cfg);
 private:
     std::ofstream fout;
     std::string analyzerInfoFile;
diff --git a/lib/checkunusedfunctions.cpp b/lib/checkunusedfunctions.cpp
index 6ddc26a55..19d0709c7 100644
--- a/lib/checkunusedfunctions.cpp
+++ b/lib/checkunusedfunctions.cpp
@@ -312,14 +312,23 @@ namespace {
     };
 }
 
-void CheckUnusedFunctions::analyseWholeProgram(ErrorLogger * const errorLogger, const std::string &buildDir, const std::map<std::string, std::size_t> &files)
+void CheckUnusedFunctions::analyseWholeProgram(ErrorLogger * const errorLogger, const std::string &buildDir)
 {
     std::map<std::string, Location> decls;
     std::set<std::string> calls;
 
-    for (std::map<std::string, std::size_t>::const_iterator it = files.begin(); it != files.end(); ++it) {
-        const std::string &sourcefile = it->first;
-        const std::string xmlfile = AnalyzerInformation::getAnalyzerInfoFile(buildDir, sourcefile);
+    const std::string filesTxt(buildDir + "/files.txt");
+    std::ifstream fin(filesTxt.c_str());
+    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)
+            continue;
+        const std::string xmlfile = filesTxtLine.substr(0,firstColon);
+        const std::string sourcefile = filesTxtLine.substr(lastColon+1);
 
         tinyxml2::XMLDocument doc;
         tinyxml2::XMLError error = doc.LoadFile(xmlfile.c_str());
diff --git a/lib/checkunusedfunctions.h b/lib/checkunusedfunctions.h
index 55c567878..8f834c86e 100644
--- a/lib/checkunusedfunctions.h
+++ b/lib/checkunusedfunctions.h
@@ -62,7 +62,7 @@ public:
     std::string analyzerInfo() const;
 
     /** @brief Combine and analyze all analyzerInfos for all TUs */
-    static void analyseWholeProgram(ErrorLogger * const errorLogger, const std::string &buildDir, const std::map<std::string, std::size_t> &files);
+    static void analyseWholeProgram(ErrorLogger * const errorLogger, const std::string &buildDir);
 
 private:
 
diff --git a/lib/cppcheck.cpp b/lib/cppcheck.cpp
index 16c497d94..352f7d412 100644
--- a/lib/cppcheck.cpp
+++ b/lib/cppcheck.cpp
@@ -153,7 +153,7 @@ unsigned int CppCheck::processFile(const std::string& filename, const std::strin
             // Calculate checksum so it can be compared with old checksum / future checksums
             const unsigned int checksum = preprocessor.calculateChecksum(tokens1, toolinfo);
             std::list<ErrorLogger::ErrorMessage> errors;
-            if (!analyzerInformation.analyzeFile(_settings.buildDir, filename, checksum, &errors)) {
+            if (!analyzerInformation.analyzeFile(_settings.buildDir, filename, cfgname, checksum, &errors)) {
                 while (!errors.empty()) {
                     reportErr(errors.front());
                     errors.pop_front();
@@ -737,10 +737,11 @@ void CppCheck::analyseWholeProgram()
 
 void CppCheck::analyseWholeProgram(const std::string &buildDir, const std::map<std::string, std::size_t> &files)
 {
+    (void)files;
     if (buildDir.empty())
         return;
     if (_settings.isEnabled("unusedFunction"))
-        CheckUnusedFunctions::analyseWholeProgram(this, buildDir, files);
+        CheckUnusedFunctions::analyseWholeProgram(this, buildDir);
 }
 
 bool CppCheck::isUnusedFunctionCheckEnabled() const