Make all projects generate a fresh project tree

Do not update the existing project tree anymore: Start a fresh one
and throw the old one away.

Change-Id: Ifabe293b6ca668b0672516a6d81acd5346d98fe5
Reviewed-by: hjk <hjk@qt.io>

src/plugins/autotoolsprojectmanager/autotoolsproject.cpp

@@ -227,8 +227,10 @@ void AutotoolsProject::makefileParsingFinished()
                              f == QLatin1String("configure.ac")) ? FileType::Project : FileType::Resource,
                             false);
     });
-    rootProjectNode()->makeEmpty();
-    rootProjectNode()->buildTree(fileNodes);
+
+    auto newRoot = new AutotoolsProjectNode(projectDirectory());
+    newRoot->buildTree(fileNodes);
+    setRootProjectNode(newRoot);
 
     updateCppCodeModel();