Improve handling of java/lang/System entry points in CG generation

OPAL/br/src/main/resources/reference.conf

@@ -75,7 +75,10 @@ org.opalj {
             {declaringClass = "java/lang/ClassLoader", name = "checkPackageAccess", descriptor = "(Ljava/lang/Class;Ljava/security/ProtectionDomain;)V"},
             {declaringClass = "java/lang/ClassLoader", name = "addClass", descriptor = "(Ljava/lang/Class;)V"},
             {declaringClass = "java/lang/ClassLoader", name = "findNative", descriptor = "(Ljava/lang/ClassLoader;Ljava/lang/String;)J"},
-            {declaringClass = "java/security/PrivilegedActionException", name = "<init>", descriptor = "(Ljava/lang/Exception;)V"}
+            {declaringClass = "java/security/PrivilegedActionException", name = "<init>", descriptor = "(Ljava/lang/Exception;)V"},
+            {declaringClass = "java/lang/System", name = "initPhase1", descriptor = "()V"},
+            {declaringClass = "java/lang/System", name = "initPhase2", descriptor = "(ZZ)I"}
+            {declaringClass = "java/lang/System", name = "initPhase3", descriptor = "()V"}
           ]
           # additional entry points can be specified by adding a respective tuple that must consist of
           # a class name and a method name and can be refined by also defining a method descriptor.
@@ -97,7 +100,8 @@ org.opalj {
           #analysis = "org.opalj.br.analyses.cg.LibraryInstantiatedTypesFinder"
 
           instantiatedTypes = [
-
+            "java/lang/ClassLoader",
+            "java/lang/Thread"
           ]
         }
       }

OPAL/br/src/main/scala/org/opalj/br/analyses/cg/EntryPointFinder.scala

@@ -258,15 +258,6 @@ trait ConfigurationEntryPointsFinder extends EntryPointFinder {
                                 )
                         }
 
-                        if (methods.exists(_.body.isEmpty)) {
-                            OPALLogger.warn(
-                                "project configuration",
-                                s"$typeName has an empty method $name); " +
-                                    "entry point ignored"
-                            )
-                            methods = methods.filter(_.body.isDefined)
-                        }
-
                         entryPoints = entryPoints ++ methods
 
                     case None if !isSubtype =>

OPAL/tac/src/main/resources/reference.conf

@@ -1329,6 +1329,81 @@ org.opalj {
           // java.lang.System                                                                     //
           //                                                                                      //
           //////////////////////////////////////////////////////////////////////////////////////////
+          {
+            cf = "java/lang/System",
+            name = "initPhase1",
+            desc = "()V",
+            pointsTo = [
+              {
+                lhs = {
+                  cf = "java/lang/System",
+                  name = "initPhase1",
+                  desc = "()V"
+                },
+                rhs = {
+                  cf = "java/lang/System",
+                  name = "initPhase1",
+                  desc = "()V"
+                  instantiatedType = "Ljava/io/BufferedInputStream;"
+                }
+              }
+            ],
+            methodInvocations = [
+              {
+                cf = "java/lang/System",
+                name = "setIn0",
+                desc = "(Ljava/io/InputStream;)V"
+              },
+              {
+                cf = "java/lang/System",
+                name = "setOut0",
+                desc = "(Ljava/io/PrintStream;)V"
+              },
+              {
+                cf = "java/lang/System",
+                name = "setErr0",
+                desc = "(Ljava/io/PrintStream;)V"
+              },
+              {
+                cf = "java/lang/System",
+                name = "newPrintStream",
+                desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;"
+              }
+            ]
+          },
+          {
+            cf = "java/lang/System",
+            name = "newPrintStream",
+            desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;",
+            pointsTo = [
+              {
+                lhs = {
+                  cf = "java/lang/System",
+                  name = "newPrintStream",
+                  desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;"
+                },
+                rhs = {
+                  cf = "java/lang/System",
+                  name = "newPrintStream",
+                  desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;",
+                  instantiatedType = "Ljava/io/PrintStream;"
+                }
+              },
+              {
+                lhs = {
+                  cf = "java/lang/System",
+                  name = "newPrintStream",
+                  desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;"
+                },
+                rhs = {
+                  cf = "java/lang/System",
+                  name = "newPrintStream",
+                  desc = "(Ljava/io/OutputStream;Ljava/lang/String;)Ljava/io/PrintStream;",
+                  instantiatedType = "Ljava/io/BufferedOutputStream;"
+                }
+              }
+            ]
+          },
           {
             // assigns its parameter to the field System.in
             cf = "java/lang/System", name = "setIn0", desc = "(Ljava/io/InputStream;)V",

OPAL/tac/src/main/scala/org/opalj/tac/cg/PropagationBasedCallGraphKeys.scala

@@ -9,8 +9,8 @@ import org.opalj.br.analyses.cg.InitialInstantiatedTypesKey
 import org.opalj.br.fpcf.FPCFAnalysisScheduler
 import org.opalj.br.fpcf.properties.SimpleContextsKey
 import org.opalj.tac.fpcf.analyses.cg.PropagationBasedTypeIterator
-import org.opalj.tac.fpcf.analyses.cg.rta.ConfiguredNativeMethodsInstantiatedTypesAnalysisScheduler
 import org.opalj.tac.fpcf.analyses.cg.xta.ArrayInstantiationsAnalysisScheduler
+import org.opalj.tac.fpcf.analyses.cg.xta.ConfiguredNativeMethodsInstantiatedTypesAnalysisScheduler
 import org.opalj.tac.fpcf.analyses.cg.xta.CTASetEntitySelector
 import org.opalj.tac.fpcf.analyses.cg.xta.FTASetEntitySelector
 import org.opalj.tac.fpcf.analyses.cg.xta.InstantiatedTypesAnalysisScheduler
@@ -61,7 +61,7 @@ trait PropagationBasedCallGraphKey extends CallGraphKey {
             new InstantiatedTypesAnalysisScheduler(theTypeSetEntitySelector),
             new ArrayInstantiationsAnalysisScheduler(theTypeSetEntitySelector),
             new TypePropagationAnalysisScheduler(theTypeSetEntitySelector),
-            ConfiguredNativeMethodsInstantiatedTypesAnalysisScheduler,
+            new ConfiguredNativeMethodsInstantiatedTypesAnalysisScheduler(theTypeSetEntitySelector),
             TriggeredFieldAccessInformationAnalysis,
             ReflectionRelatedFieldAccessesAnalysisScheduler
         ) ::: (if (isLibrary) List(LibraryInstantiatedTypesBasedEntryPointsAnalysis) else Nil)

OPAL/tac/src/main/scala/org/opalj/tac/fpcf/analyses/cg/ConfiguredNativeMethodsCallGraphAnalysis.scala

@@ -82,9 +82,7 @@ class ConfiguredNativeMethodsCallGraphAnalysis private[analyses] (
         // we only allow defined methods
         if (!dm.hasSingleDefinedMethod) return NoResult
 
-        val method = dm.definedMethod
-
-        if (!method.isNative || !nativeMethodData.contains(dm)) {
+        if (!nativeMethodData.contains(dm)) {
             return NoResult;
         }