During development, it is quite common to have to start with a fresh repository. Usually this is because you've made a significant change to the model, and you'd rather blow everything away than clean up inconsistencies. The Alfresco repository is made up of two parts: the metadata stored in the relational database and the binary files stored on the file system. To clear out the repository, you have to clear out both. If you delete the data directory but not the database, you will see a bunch of data integrity problems because the binary files that the database knows about are no longer there.

The extras directory in your Alfresco distribution has scripts you can use to quickly drop and recreate the database. Some people find it convenient to create a script that executes the remove database script, then create database script, and then purges the data directory.