Make the ITS rule set a project attribute not a tool level attribute. Different projects will have different sets of ITS rules. Shouldn't have to share one set of ITS across all projects.
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The selection of what ITS rules to use can be set per file, even per file of the same XML format. Use the parameters files for this: An input XML file can be associated to a parameters file, which can indicate what ITS rules file to use (using the "use the following ITS file" in the dialog). different parameters file can be saved for each project.
Is this answer you concern for project-level settings?