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Will this plugin work with my theme's galleries?

Possibly. WP Gallery Custom Links plugin was designed for use with 1) WordPress's [gallery] shortcode and 2) images attached to the post/page. Some themes use these features, and others have their own proprietary way of saving gallery images and drawing out the gallery. Provided your theme meets the criteria above, the plugin should work with it.

Will this plugin work with NextGen galleries?

No, this plugin is not compatible with NextGen galleries. WP Gallery Custom Links was designed for use with 1) WordPress's [gallery] shortcode and 2) images attached to the post/page. NextGen galleries uses its own [nggallery] etc. shortcodes that function outside of the WordPress [gallery] shortcode.

I've set my gallery to remove Lightbox effects, but they are still coming up. Why?

Your Lightbox javascript may be running after the WP Gallery Custom Links javascript. This may cause the Lightbox effect to be applied after the WP Gallery Custom Links script attempts to remove it. Try moving your Lightbox javascript above the WP Gallery Custom Links javascript. Note that you may need to add your Lightbox script as a dependency for WP Gallery Custom Links to make sure WP Gallery Custom Links runs after it.

When I enable the plugin, the styling on my gallery changes. Why?

The way the plugin works requires the gallery generation code to be run twice. This may result in it being labeled as "#gallery-2" instead of "#gallery-1." Check your HTML and CSS for these changes and adjust accordingly.