The location of the database files is defined by the url attribute of the Resource element jdbc/Main in the context file defining the application in tomcat.
However, I think the issue is not file permissions, but rather that your .script file is missing a definition of the USERS table, or that the definition is incomplete, when compared to the definition in the model. To overcome this you can either copy a complete definition (or the database files as a whole, as maintained in the studio - see the "database" subfolder of the application project), or instruct the server do the same as the studio (i.e. create table definitions or add the necessary columns to an existing table definition) by adding the folllowing to the context file:
Whatever you do, ensure you stop the application/tomcat, and backup existing database files
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