Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py
Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py

Completed integration & unit testing
Merge remote-tracking branch 'upstream/master' into flortd_dev
Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py

Completed integration & unit testing
Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py

Completed integration & unit testing
Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py

Completed integration & unit testing
Merge remote-tracking branch 'ooici/master'

Conflicts:
	.gitignore
	.gitmodules
	Doxyfile
	README
	autolaunch.cfg
	build.xml
	buildout.cfg
	extern/coverage-model
	extern/ion-definitions
	extern/ion-functions
	extern/pyon
	res
	setup.cfg
	setup.py

Completed integration & unit testing
Qual testing complete EXCEPT test_capabilities
completed qual testing
re-wrote particles
TODO - all testing
removed params.py OBE
implemented acquire sample
all broken
removed unused imports & fixed apply_startup_params
Merge pull request #169 from rmanoni/flortd_dev

Flortd dev code review