private void doSynchronize() {
			try {
				rootFolderData.refresh(true, true, projectDisposalMonitor);
				scheduleUserDataReconcilation();
			}
			catch (Exception e) {
				Msg.trace(this, "Exception synchronizing filesystem", e);
			}
		}
Reconcile user data files against all content files within the project.
This must only be done while connected to the repository
Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DefaultProjectData.java