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> 2/ how can I implement atexit like stuff in Lua ?

Set a gc metamethod for a table that is keep safely in a global variable.
> 3/ is this function called even when the daemon will receive a SIGQUIT
> signal ?

The standard Lua interpreter does not handle SIGQUIT. You can either
change it or use your own Lua host. You can also try to do signal
handling using luaposix.