Bug after Recent Update to 3.0.0 from 2.1.4
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Version 3.0.0 exhibits the following issue after an upgrade from 2.1.4.
If you modify (eg. change the name) a taxonomy term assigned to a CPT (in my case, a custom hierarchical taxonomy) using the WP back-end, the permalink for that category is reverted to an unexpected /index.php/taxonomy-slug/term-parent-slug/term-parent-slug/term-child-slug rather than the expected permalink as configured using your plugin, eg. /cpt-slug/term-parent-slug/term-child-slug/cpt-item.
If I re-save the WP Better Permalink settings (they were preserved during the upgrade), the issue still exists.
I easily duplicated this on a clean WP instance using Toolset Types to create a custom post type and taxonomy using the defaults.
If I delete the plugin and upload 2.1.4, the issue does not present itself.
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