Removed last of XFT and other preference settings, cleaned up some code references.

src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java

src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java

src/main/java/org/nrg/viewer/QCImageCreator.java

src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java

src/main/java/org/nrg/xnat/archive/BatchTransfer.java

src/main/java/org/nrg/xnat/archive/Transfer.java

.../java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java

...va/org/nrg/xnat/notifications/NotifyProjectListeners.java

...rg/xnat/notifications/NotifyProjectPipelineListeners.java

src/main/java/org/nrg/xnat/restlet/XNATApplication.java

...n/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java

...rg/nrg/xnat/restlet/extensions/AuthenticationRestlet.java

...org/nrg/xnat/restlet/resources/ProjectMemberResource.java

...nrg/xnat/restlet/resources/ProjtExptPipelineResource.java

...n/java/org/nrg/xnat/restlet/resources/SecureResource.java

.../java/org/nrg/xnat/restlet/services/mail/MailRestlet.java

...ervices/messaging/file/MoveStoredFileRequestListener.java

...java/org/nrg/xnat/turbine/modules/actions/AddProject.java

...org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java

.../org/nrg/xnat/turbine/modules/actions/ManagePipeline.java