The applications in the jstools suite can be customised in several ways, including preferences panels, startup scripts, and X defaults.
Preferences
All supported jstools applications (and to some extend other applications that use the jstools libraries) recognise the preferences set through the Global Preferences panel (q.v.). This is normally available on the application's leftmost menu; it is also accessible through the standalone jprefs application. Most applications also have an application¡specific preferences panel, which will also be available on the application's leftmost menu. (The jedit editor has three levels of preferences; in addition to global and application¡specific preferences, it supports additional preferences for various types of files.)
(Preferences are stored in files under your ~/.tk directory (the directory .tk under your home directory). Global preferences are stored in the file ~/.tk/defaults. Application¡specific defaults for each application are stored in the file ~/.tk/app-defaults, where app is the name of the application. You shouldn't need to edit these files by hand.)
Startup Scripts
Most jstools applications support an application¡specific startup script in Tcl, called ~/.tk/apprc.tcl. This script contains additional Tcl code that the application will execute when it starts up. Exactly what it's appropriate to put in here varies from application to application, but in general you can redefine procedures used by the application to change their behaviour. The documentation for each application that can be customised in this way will have more information.
In order to write application¡specific startup scripts effectively, you'll need to know Tcl and Tk, and you may need to know something about the structure of the application. The book Tcl and the Tk Toolkit by the author of Tcl, John Ousterhout, (New York: Addison¡Wesley, 1994) is a good introduction to programming in Tcl, although you'll also need to refer to the manl pages. You may also find that you can pick up enough by examining the jstools scripts themselves.
The jstools applications also support a special¡purpose startup scripts ~/.tk/textbindings.tcl and ~/.tk/entrybindings.tcl. These are intended to supplement the keyboard bindings used by the applications, so you can make minor changes to them. Unfortunately, I haven't written documentation about how to do this yet. (You can include ordinary Tcl bind commands, but that may break things like jedit's special interpretation of punctuation and the Return key, or other special features of the bindings libraries. I hope to document this in a future version.)
Sample configuration files
If jstools was installed normally at your site, there will be a few sample configuration files in the directory samples in the jstools library directory (typically /usr/local/lib/jstools).
X Defaults
You can also change the general appearance of the jstools applications (and other Tk applications) using the X defaults mechanism. For reference, here are the defaults I use for Tk widgets:
