[BZ 1038728] [BZ 782915] Add required DOCTYPE declaration back, but do not use it on indenting phase

(cherry picked from commit d6c14baa1bc2f4b8e63045abe10bf4d62878708c)
Signed-off-by: Libor Zoubek <lzoubek@redhat.com>

Conflicts:
	modules/enterprise/agent/src/test/java/org/rhq/enterprise/agent/AgentConfigurationTest.java