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Since version 1.5, you don't need to poke around PHP files anymore just to add an id or change a class.
The widget uses a series of Mustache templates, which are very easy to understand, if you know HTML.
Here's how you would change those templates to better fit into your theme:
- In your theme directory, create a subdirectory called qmt-templates.
- Copy the file(s) from query-multiple-taxonomies/templates into that subdirectory.
- Modify the copied file to suit your needs.
By doing it this way, you won't loose your customizations when you update the plugin.