Description of problem:
Modifying the same deployment through the CLI and deployments/ can get the deployment into an incorrect state.

Version-Release number of selected component (if applicable):
6.2

How reproducible:
Always

Steps to Reproduce:
1.  Put deployment (test.war) in deployments/ so it will be deployed
2.  "undeploy --keep-content test.war"
3.  "deploy --name=test.war"
4.  Restart EAP

Actual results:
test.war is not deployed because step 2 created test.war.undeployed, but step 3 did not remove it.

Expected results:
test.war is deployed

Additional info:

I also saw some other problems when modifying the same deployment through both deployments/ and the CLI, but haven't replicated them yet.