I'm currently using Spring Tool Suite (STS) (Version: 3.6.3.CI-B2266066, Build Id: 201411050946, Platform: Eclipse Luna SR1 (4.4.1)) with Spring Integration 4.1.0.
I have a Spring configuration XML file that includes the Spring Integration namespace. I go into the integration-graph tab and go into "manual layout" mode to spruce-up my flow. If I then turn "Enable Automatic Layout" back on the graph reverts back to how it looked before I made my manual edits. If I then go back into "manual layout" mode my edits are still saved. That works as expected.
It appears that the automatic-layout is somewhat tied to the order that elements are defined within the Spring context XML file itself. Meaning that if I change the order of elements within the XML file the layout on the graph will also change. It might be a nice feature to allow someone to perform some manual layouts then have the editor do a best-effort to save those edits to the underlying XML file. We have some decent sized XML files and often use the automatic-layout mode. It's cumbersome to then have to manually move things around in the XML file to make the layout show properly in the graph. I know not all edits would be able to be saved in the XML file (i.e. exact positioning and edits would be lost) but some of the edits probably could be saved (i.e. this channel needs to be defined above this channel in the XML file since it's showing in the manually-edited graph above that channel.
Perhaps there's a way to do that already that I'm missing?
No, there is no way to edit this graph manually... If this is allowed then the layout data needs to be persisted somehow. There is a possibility of adding more layouts to chose from from the GEF Zest project. This could be an alternative for what you are asking. Please submit a JIRA request for enhacement against Spring Tool Suite project :-) (https://issuetracker.springsource.com/browse/)