There were (and still are) many divisions in Hinduism. According to historical facts, these divisions were very deep rooted in the society during the Medieval period. It is also known that there were serious clashes between them.
In South India, especially during the Chola rule, there were four main religions. Buddhism, Jainism, Saivism and Vaishnavism (yes, Saivism and Vaishnavism were separate religions back then, atleast that's what history says). There were clashes between Saivism and Vaishnavism. For instance, King Kulothunga Chola II ordered to uproot Govindaraja Swamy from Thillai Nataraja temple (a Saivite temple). Then during the 16th century, Krishnappa Nayak seems to have ordered the re-installation of Govindaraja in the temple, amidst strong protests from the Saivites.
Though Buddhism and Jainism have maintained their status as separate religions, Saivism and Vaishnavism, once clashing sects, are now united under Hinduism. Today, there is no enemity among Saivites and Vaishnavites, as far as I know. The Saivites visit Vaishnavite temples and Vaishnavites pray at Saivite temples. Even other sects like Shaktism, Kaumaram easily mingle with others.
What or who led to this unification of once clashing divisions of Hinduism?