http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5625

--- Comment #4 from Daniel Crawl <[email protected]> ---
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

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