A few system shell built-ins invoke jEdit features:
%browse [-n|--new-window] directory: opens the specified directory in jEdit's file system browser. If -n or --new-window is specified, opens a new floating instance of the file system browser.
%edit files ...: opens the specified files in jEdit.
%run scripts ...: runs the specified script files. You can run BeanShell scripts, or any script type supported by an installed plugin (for example you can run Python scripts if JythonInterpreter is installed).