JBIDE-16505 - did not remove deployment marker when module removed

JBIDE-16505 test case

Changes as requested from PR comments

Changes as requested from PR comments

Changes as requested from PR comments
JBIDE-16504 rse profile must make explicit which publish subsystem
should be used

JBIDE-16504 - test case
JBIDE-16507 - LocalFilesystemController uses incorrect temporary
deploy folder

JBIDE-16507 - not using agreed upon temp file

JBIDE-16507 - add test case