What I do is a partially hard-coded trick: I use a file that I require_once just after the reloadSettings(); in index.php, the file looks something like:
init_CertainAddon();
function init_CertainAddon()
{
$hooks = array(
array(
'integrate_some_hook',
'the_integration_function',
'SOURCEDIR/CertainAddon.integrate.php',
),
);
foreach ($hooks as $hook)
add_integration_function($hook[0], $hook[1], $hook[2], false);
}
The "trick" is the last "false" of the add_integration_function, that tells the system not to store permanently the hook, that way I just need to change that file and the hooks are updated automagically.
Then, when the development is finished, I copy the array of hooks into the installation code of the addon and that's it, ready to ship.
The advantage of having each addon enclosed in a function is that I can enable/disable them just by commenting or de-commenting the line that calls the function.
HTH!