Ensure that the actual project file is only only overwritten, when th…

…e saving process was successful and not interrupted

* Strategy to achieve this:
 * When saving the mastodon project file, it is first saved to projectname.mastodon_pending
 * When saving to this file was successful, projectname.mastodon gets overwritten with projectname.mastodon_pending
 * In the past, it has been observed that *.mastodon files were corrupted and could not be read anymore
 * Typical saving times for a project range from ~0.2s to ~2s (depending on project size, attributes, etc.). Not very long, but long enough to kill mastodon during the saving process.

src/main/java/org/mastodon/mamut/io/ProjectSaver.java

@@ -73,6 +73,7 @@
 import org.mastodon.ui.util.FileChooser;
 import org.mastodon.ui.util.FileChooser.SelectionMode;
 import org.mastodon.util.BDVImagePlusExporter;
+import org.mastodon.util.FileUtils;
 import org.mastodon.views.bdv.SharedBigDataViewerData;
 import org.scijava.Context;
 
@@ -256,8 +257,14 @@ public static synchronized void saveProject( final File saveTo, final ProjectMod
 		final MamutProject project = appModel.getProject();
 		final File tmpDatasetXml = ProjectLoader.originalOrBackupDatasetXml( project );
 
+		// Save to a temporary file or directory first.
+		String suffix = "_pending";
+		File saveToPending = FileUtils.createFileOrDirectoryWithSuffix( saveTo, suffix );
+		if ( saveToPending == null )
+			saveToPending = saveTo;
+
 		// Possibly update project root.
-		project.setProjectRoot( saveTo );
+		project.setProjectRoot( saveToPending );
 		try (final MamutProject.ProjectWriter writer = project.openForWriting())
 		{
 			MamutProjectIO.save( project, writer );
@@ -272,6 +279,11 @@ public static synchronized void saveProject( final File saveTo, final ProjectMod
 			// Set save point.
 			model.setSavePoint();
 		}
+		project.setProjectRoot( saveTo );
+		Files.delete( saveTo.toPath() );
+		boolean success = saveToPending.renameTo( saveTo );
+		if ( !success )
+			throw new IOException( "Could not rename " + saveToPending + " to " + saveTo );
 
 		// Save BDV settings.
 		// Imperfect because a full saving requires have a view opened,