Is it permissible to deal with a company based in Israel that includes Arab and Jewish employees, which acts as an intermediary to introduce software companies to potential clients around the world (Jewish, Arab, English), in exchange for a percentage of the profit?

The basic ruling is that it is permissible to deal with companies that employ both Arab and Jewish staff, provided that the dealings are not in a forbidden matter. The Prophet, peace and blessings be upon him, dealt with Jews, and he passed away while his shield was mortgaged to a Jew. A condition for your dealings with these companies is that the programs or websites you provide them with are not used for a forbidden purpose. However, a boycott may become obligatory if Muslims believe that not boycotting strengthens enemies against Muslims.