I have been thinking about making such a aplication too. Never did it but I came to this conclusion.

Either make it a login page and make very sure your login is secure. Or make all of it button and selectable options. Make ABSOLUTLY sure that all the assembling of the command line code is done in the PHP code itself.

Also (my information on linux shell commands is lacking here) things like making a search command and allowing a user to input a search string of his own should be very well checked for it may pose an opertunity to sneak in more commands.

Have fun making this.