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The Project Settings include adjustments for the whole project. To open the dialog go to the Edit menu in WD and choose "Project Settings". More project settings can be found under File menu > Profile.
Tick "Run on System Start" if you would like the project to automatically open after your system finished booting.
"Activate Skinning" loads the dark skinning of the WD application. Restart WD after changing this option.
If you like to run a script (consisting of one or more commands) each time the project is loaded, add the commands to the text box and tick the check box "Execute Startup Script". The topic Script Language explains commands and how to use them in more detail. Tip: You may use a macro.