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pnpm store prune does clean the dlx cache, but only entries older than dlxCacheMaxAge. The default is 1440 minutes (one day), so a package you ran with pnpx a moment ago is kept.

There is also a bug. store prune prunes the store first and only then removes the expired dlx cache entries. The dlx cache entry still links its packages into the store while the store is pruned, so those packages survive until the next pnpm store prune. We are fixing this so a single pnpm store prune removes the expired entries and the packages only they used.

Until the fix ships, you can drop the whole dlx cache right away:

pnpm_config_dlx_cache_max_age=0 pnpm store prune
pnpm store prune

Or delete $(pnpm confi…

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@rafern
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