What is the ruling on the salary of a manager who did not adhere to official working hours, believing that work is about output, not time, and what should he do to clear his conscience after repenting?

It is not permissible for an employee to be absent from work without a valid excuse. If they do so, they have committed an error and must repent and show remorse. If they believed their action was permissible, then what has passed is theirs and there is nothing upon them except repentance. It is more cautious to donate whatever remains in their possession as charity. However, if they knew their action was forbidden, they must return the money to its owners. If this is not possible, they must dispose of it by spending it on charitable causes.