Clean up uses of getConfigurationDirectory

Currently quite a few places call getConfigurationDirectory() to find out the default directory for locating data etc.  It does this by looking up information in the environment.xml.  That doesn't work for the cloud version of the system.

Some possible stages.

• Replace calls to envGetConfigurationDirectory with getConfigurationDirectory
• Create functions for each of the different catageories and call those instead
• Simplify the parameters to each of those functions
• Implement those functions for containerized builds.