Oh, too many eclipse directories. There're two different main(eclipse) directories here, one for the Eclipse installation and one for the JBossIDE installation.
The directory which contains eclipse/links/ is just "fresh" Eclipse installation (contains the executable eclipse file and all the base features and plugins ).
And the directory which contains .eclipseextension doesn't contain anything else than .eclipseextension, features and plugins. So two different locations.
This solution keeps your (real) Eclipse installation directory clean and also allows multiple Eclipse installations to use the same JBossIDE installation.
Almost forgot the request ;)
Provide downloadable JBossIde zip which contains all the JBossIDE features/plugins packaged in the way described above (nodeps). And maybe a template links/org.jboss.eclipse.lnk file. Then all that needs to be done is to edit the lnk file with a proper path pointing to the unzipped directory and (re)start Eclipse with JBossIDE powers.