To check a configuration file without actually publishing its results, run:
domtool -tc $FILENAME
Here, -tc stands for "type-check." The Domtool language is designed to capture all rules of which configuration is valid and which isn't in its parsing and typing rules, so using the -tc option should enable you to find any bugs in your configuration. We might have bugs in our implementations of the configuration directives from time to time, but -tc should be sufficient to help you find your own bugs.
Note that using your ~/.domtool directory as a scratch space with lots of stray files is a bad idea, especially if you have multiple files representing different alternatives for configuring the same domain. Sometimes we make a change to Domtool that requires reprocessing all user configuration. In such cases, we run every file found in any user's ~/.domtool directory. In that case, your ~/.domtool files will be run in an arbitrary order, including any files that you have been thinking of as "test cases." It just might happen that the "test cases" end up overriding the "real" files. In summary, use another directory for storing tests, and run them by specifying explicit filename arguments to domtool, possibly with the -tc option.