Kepler

We should verify all the exercises in the getting started guide. While updating it for 5452, I noticed that the Run Window is no longer accessible.

Fix references: FSM -> Modal and CT -> Continuous.
SDF default iterations is now 1.

Add new command-line options for executing KARs, redirecting display actors, etc. See the full list here: https://kepler-project.org/developers/reference/executing-kepler-from-the-command-line/

Jianwu and I have updated the documentation, including:

- references and screenshots of CT > Continuous
I didn't see any references to FSM
- add new options for command-line execution

Still to do:

- update section 6.9: the demo workflow no longer reads the gene sequence from a web service.
- recreate figure 4.23: too blurry to be useful.
- assemble into a single PDF and check in to common/configs/.../UserManual.pdf

Dan and I created user manual documentation 2.4 at kepler doc trunk r1412.

user manual documentation is also checked into kepler trunk at common module. closing the bug.

Original Bugzilla ID was 5625