Regenerate primary key when making layer permanent if layer property set

Respect the OnConvertFormatRegeneratePrimaryKey layer property when
making a temporary layer permanent.

This ensures that processing outputs which require primary key
regeneration will correctly get new primary keys when they are
initially run with a memory layer output, and then later that
memory layer is made permanent

Fixes #58942

src/app/qgisapp.cpp

@@ -8328,6 +8328,10 @@ void QgisApp::makeMemoryLayerPermanent( QgsVectorLayer *layer )
         source += QStringLiteral( "|layername=%1" ).arg( newLayerName );
       vl->setDataSource( source, vl->name(), QStringLiteral( "ogr" ), options );
       vl->triggerRepaint();
+      // we don't want this flag anymore -- the layer has changed format and from now on
+      // primary keys should be retained if it's exported to a new file
+      vl->removeCustomProperty( QStringLiteral( "OnConvertFormatRegeneratePrimaryKey" ) );
+
       mLayerTreeView->refreshLayerSymbology( vl->id() );
       this->visibleMessageBar()->pushMessage( tr( "Layer Saved" ),
                                               tr( "Successfully saved scratch layer to <a href=\"%1\">%2</a>" ).arg( QUrl::fromLocalFile( newFilename ).toString(), QDir::toNativeSeparators( newFilename ) ),
@@ -8608,8 +8612,14 @@ QString QgisApp::saveAsVectorFileGeneral( QgsVectorLayer *vlayer, bool symbology
     options.saveMetadata = dialog->persistMetadata();
     options.layerMetadata = vlayer->metadata();
 
+    QgsFeatureSink::SinkFlags sinkFlags;
+    if ( vlayer->customProperty( QStringLiteral( "OnConvertFormatRegeneratePrimaryKey" ) ).toBool() )
+    {
+      sinkFlags.setFlag( QgsFeatureSink::RegeneratePrimaryKey, true );
+    }
+
     bool addToCanvas = dialog->addToCanvas();
-    QgsVectorFileWriterTask *writerTask = new QgsVectorFileWriterTask( vlayer, vectorFilename, options );
+    QgsVectorFileWriterTask *writerTask = new QgsVectorFileWriterTask( vlayer, vectorFilename, options, sinkFlags );
 
     // when writer is successful:
     connect( writerTask, &QgsVectorFileWriterTask::completed, this, [onSuccess, addToCanvas, encoding, vectorFilename, format]( const QString & newFilename, const QString & newLayer )