EAP6.0 had a bug where it would not pick up deployments done via the filesystem. Please try EAP 6.0.1 (or AS7.1 since the bug was introduced late).
Since yes, JBoss Tools create the .dodeploy folder, but it is then AS7/EAP6 "job" to remember this between restarts.
You're right, I just discovered this the other day
But, unfortunately EAP 6.0.1 doesn't work correctly with the current version of JBoss tools. I'll create a separate forum post for that.