Is your "." directory in your updateDatabase classpath? It looks like Liquibase only can find the file using the filesystem-based locator which is trying to normalize the paths.
I created https://liquibase.jira.com/browse/CORE-1682 to look into it more, but it usually works best to make sure your files are in your classpath. Listing your base file as "database/master.xml" may help as well too.
Nathan