...automate or build projects from the command line?

Do you have a command line tool that I can use to build CrossWorks projects without using the CrossStudio IDE?

Yes, CrossWorks includes the CrossBuild utility for this purpose.

CrossBuild can be found in the $(StudioDir)/bin directory. For more information on using CrossBuild please take a look at the Command Line Tools > CrossBuild section of the on-line documentation.