When I add OpenShift marker files (those in .openshift/markers) with Eclipse, I have found the marker files are created but not added to the Git repository. This means when you then use the IDE to Publish, the marker files are not pushed to OpenShift Online. An easy one to try to test this is Hot Deploy; if the change were picked up, this would be reflected in the console messages when the app is rebuilt.

At the moment it looks like you have to do a manual 'git add .openshift/markers/*' before the files will be picked up, and also manually remove the files from Git when you want to delete a marker. I'm not sure if this is a bug or just a missing feature, but it does mean the user has to use the command line; it would be preferable to be able to stay in the IDE and have these file changes recognised by the IDE's Publish process.