Several options are configurable from the jEdit options dialog. There are options to control the GUI of the plugin, and internal behaviour when executing several actions. The options are:
Use external applications by default: if selected, files that are open from the tree (by either double-clicking or middle-clicking) will be opened using the external application configured for the file's extension, if any. If no application is found, it will be opened in jEdit. You can still open the file in jEdit by dragging the file node onto jEdit's text area. When opening in an external application, you'll lose support for auto-closing the file on project file, auto-loading the file when the project is re-activated and the file node won't be underlined, indicating it is opened..
Close files on project change: if selected, files from the current project that are opened in jEdit will be closed when you switch to another project.
Remember open files: if selected, files opened in the current project will be re-opened when you select the same project in a later moment, even between different jEdit sessions.
Delete non-existant files from list: if selected, each file in the project is verified to exist when the project loads. If the file does not exist, it is removed from the project.
Ask to import new files: if "Always" is selected, every time you save a file located below the active project's root, and the file is not yet part of the project, you'll be asked whether you want to import it. Selecting "Once per session" will ask only one time during the time the current project stays active. "Never" will disable this feature. "Auto import" will automatically add to the project any saved files which are under the project root and are not currently part of the project.
Show toolbar: whether to show the plugin's toolbar or not. The toolbar is automatically hidden when no tree is selected for showing, regardless of this option.
Show folders tree: if the "Folders" tree view should be shown.
Show files tree: if the "Files" tree view should be shown. Disabling this view can greatly improve performance when your projects have many files.
Show working files tree: if the "Working Files" tree view should be shown.
Show compact tree: whether the "Compact" tree view should be shown.
Show filtered tree: whether the "Filtered" tree view should be shown.
Use system icons for files: instead of using jEdit's icons, uses the system provided icon for each individual files. The jEdit icon will still be used when the file is opened. In some systems, the system icons may not be accessible from Java, so this option may not work as expected. Also, this option is only available if Java 2 version 1.4 or later is being used.
Show project (or group) name in the view's title bar: if selected, the jEdit window title will be updated with information about the currently active project or group in that window.
This controls the behaviour of the "Import settings" filter available when importing files.
Files to include: a list of globs that match files you want to include in a project (e.g., "*.html", "*.java", "README*"). If you want to exclude files from the automatic import, prepend the glob with the "!" character (e.g., "!*.class").
Directories to ignore: space-separated list of globs to match directory names to ignore when doing automatic import of files. No files within directories whose names are listed here will be imported.
Use InfoViewer's browser settings: if you have the InfoViewer plugin installed, you can choose to check this box, and when asking to open a file in a web browser, InfoViewer is going to be used to launch you browser of choice.
Browser path: the path to the web browser to be used for viewing selected files, with any needed command-line switches, in case you don't want to use the same settings as the InfoViewer plugin.
ProjectViewer provides an interface similar to jEdit's context menu editor, where you can add actions to be displayed in the trees' context menus. You can't remove the default entries in the context menu, but any action available to jEdit can be added. It's important to notice that adding an action to the context menu won't make it "Project Viewer aware": unless the action is specifically written to interface with ProjectViewer, it will work the same way as it would if executed from any other place (such as the jEdit toolbar or menu).
The "External Applications" option pane can be used to register applications you want to use for specific file type, accessible through the "Open with..." context menu command for files. Just add a file name glob and choose the application you wish to use for that entry.
The filtered view allows you to group files according to their names. To create a filter, go to the Plugin Options and choose the "Filtered view" pane, or go to the project properties dialog and choose the "Filtered view" pane, to create project-specific filters.
To create a filter, provide a file name glob (see jEdit's documentation for the supported glob syntax) and a name for the filter. If the "Show filtered tree" option is enabled, a new "virtual directory" with the filter name will be available in the "Filtered" tab of the ProjectViewer window, containig all file names that match the glob. Files that match more than one filter will be listed several times in this view.