Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
Is prayer nullified by having thoughts while performing it?
Prayer isn`t nullified by having thoughts while performing it, provided that the praying person offers all of its pillars and meets all of its conditions. However, the reward decreases significantly in the absence of reverence since a praying person is rewarded according to the attentiveness of his/her heart during prayer.
Is a wife considered sinful if she asked for divorce because her husband married another woman?
A second marriage is lawful, and so it is impermissible for you to ask for divorce because of that. If you are certain that you won`t be able to deliver Allah`s rights and those of your husband`s , then it is permissible for you to ask for Khul`a (Divorce on the demand of the wife). However, you should exercise patience since after difficulties, there is easiness by the will of Allah.
The supplication: "O Allah, we do not ask You to avert the decree, but we ask You for kindness in it." Is this Supplication Halal or Haram?
We are obliged to supplicate Allah, so when supplicating we comply with Allah's Ordainments, and making supplications that are reported in the authentic texts is better. And Allah Knows Best.
