Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible to make ablution without answering the call of nature after waking up?
Washing front and back openings (Istinjaa`) is not a condition for the validity of ablution because it is done to remove Najaasah (impurity), thus if there is no Najaasah, there is no need for that, and then it is permissible to make ablution without answering the call of nature. However, prayer is invalidated if there is Najaasah on the anus ,or the front opening, so it (Najaasah) must be removed for the prayer to become valid, and not the ablution.
Is it permissible to trim the eyebrows if they become excessively long?
Trimming eyebrows is permissible if they become excessively long, yet; it is reprehensible. And Allah Knows Best.
What is the ruling on someone who eats or drinks thinking that the sun has set, then realizes that it has not yet set?
Whoever eats or drinks believing that the sun has set, then later discovers that it has not yet set, their fast is invalid, and they must make up that day after Ramadan. It is not permissible to break the fast before confirming sunset—either by seeing it, through personal reasoning, or by relying on the statement of someone trustworthy in their religious commitment.