What is the ruling on working for an investment company that provides transportation, meals, clothing, and gifts to its employees, and deposits funds in banks to cover salaries and other expenses?

If the company's activity is permissible, and your job does not involve direct engagement in or intentional assistance with something forbidden, then there is no harm in working for it and benefiting from what is given in return. It does not matter if the company's money is mixed due to its deposits in riba-based banks, as the sin of that falls upon the company, not on the employee, as long as his work is permissible.