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In 1.13 most of the indexes now use triggers in the DB to track when changes are made to entities and the indexes are updated via cron selectively for just the entities that have changed.

The Product Attributes index was left out of this scheme however (this is the index that drives the filtered navigation):

Mage_CatalogIndex_Model_Indexer_Eav

I'm just trying to figure out why this would be the case - the EAV attributes for products are tracked in the new scheme and the catalog_product_flat_* tables are updated via the cron.

Only thing I can figure is that the update of the Product Attributes seems to put a lock on the cataloginventory_stock_item table which could cause checkout issues, but I'm wondering if there was another reason why this index couldn't be kept in check dynamically?

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Magento implemented this, but they didn't finish the task until the release. This will be released with the next minor update. At least I expect that.

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