JAL-3662 simple fix for CLI not using right format for output of alignment.

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CR-JAL-229 3

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    Participant Role Time Spent Comments Latest Comment
    Author 0m    
    Reviewer - 100% reviewed 7m 3 (1 defect) Will merge in my own patch here - you need to verify that...
    Reviewer - 0% reviewed      
    Total   7m 3 (1 defect)  
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    Objectives

    29bd435069afb8ed662313d810b03c75c830a140: JAL-3662 simple fix for CLI not using right format for output of alignment.

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    /src/jalview/bin/Jalview.java Changed 3

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