The Edit menu has commands to clear and save the output log:
Clear Output Log — Clears the information from the output log. Each time you select Create or Configure, Agent Builder appends status messages to the output log. If you are engaged in an iterative process of making changes to your source code and regenerating output in Agent Builder and want to segregate the status messages, you can save and clear the log file before each use.
Save Log File — Save the log output to a file. Agent Builder provides a browse screen that enables you to choose the directory and specify a filename.