Here's the Klicko preferences tab:

The popup menu in the window title is important. If it's set to "Excluded Applications", all windows belonging to the applications listed in the window won't be affected by Klicko; if it's set to "Included Applications", only those applications will be affected. That is, the popup changes the nature of the application list. Usually, you would set it to "Excluded" and list only the (hopefully few) applications you find incompatible.
You can add any running application by clicking on the "+" button; a pop-up menu will appear. You can also drag applications (running or not) from the Finder into (and out of) the window, of course. If you have several copies of an application installed, putting one of them in will work for all. In the example above, Klicko won't affect any of Safari's windows. Note that if you set the pop-up to "Included Applications", and put no application into the list, Klicko will have no effect at all.
Klicko has three functions which can be individually enabled, as you see in the preferences:
- Block click-through in inactive windows (see exceptions below)
- Bring all windows of an application forward by control-option-command-clicking on any of them; this also lets you bring all Finder windows forward by control-option-command-clicking on the desktop
- Maximize windows with the Zoom button; may not work for all applications
Beyond that, at any time you can direct any click to a window by holding down any modifier key. Some applications don't use standard windows or use them in a way that Klicko can't activate properly; if you find that clicking on a window has no effect at all, hold down a modifier key and try again, or try the exclusion list. Here are some known problem applications (which are added to the exclusion list automatically):
- Adobe Photoshop: fails to accept clicks in the main window while auxiliary windows like "Color Range" are on top.
- Aperture: fails to accept clicks after exiting full-screen mode.
- iMovie: accepts no clicks at all in the main window.
Klicko relies on the Accessibility interface, but you don't have to turn it on the System Preferences. Some applications may not implement Accessibility in a way that Klicko understands, and so one or all of the functions may not work properly for those. Please use the exclusion list in such a case.
Note that there's no way to disable the highlighting of the window "traffic light" buttons, so, to minimize user confusion Klicko always allows click-through on those buttons. Klicko will also always pass through clicks on windows belonging to background or full-screen applications, to dialogs, palettes, and similar interface elements, and to the Finder desktop.
Note that with click-through blocking, if you want to start a drag from a background window (say, a Finder window), you must hold down any modifier key first.
Code Signing: Klicko is codesigned for extra security. Basically, this means that you can verify if the application's executable has been signed by a specific developer, and that you can have some assurance that code or resources have not been tampered with by third parties.
To check that Klicko's signature is intact, open Terminal, paste in the following command, and press the Return key:
codesign -dvvv -r- /Library/PreferencePanes/Klicko.prefPane
(assuming that you installed Klicko for all users; otherwise, type a tilde (~) before the /Library part.) You should see several result lines in the Terminal. Authority=Rainer Brockerhoff should be present, and identify the author. The last line should end with ...root = H"4cbb97c74336f7ee6aa566122a5e7688e1c725dc" and uniquely identify the author's signature. Now run the following command:
codesign -vv /Library/PreferencePanes/Klicko.prefPane
If the Klicko bundle is intact, this should display valid on disk; otherwise you'll see code or signature modified. In the latter case, throw it into the Trash.
The Klicko background application is also codesigned. To check it, just substitute its path in the commands above (note the quotes around the path, necessary because it contains a space):
codesign -dvvv -r- "/Library/Application Support/Klicko.klicko/klickod"
codesign -vv "/Library/Application Support/Klicko.klicko/klickod"