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When navigating into a certain site dir in /var/www/html/mysite, I get the following WPCLI error:

Error: The site you have requested is not installed.

But the site is basically working and surfable... So what may cause WPCLI to miss the fact it's there?...

WPCLI doesn't miss other sites, so it's a bit wired.

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There is only one function in wp-cli which will return this error and it is wp_not_installed

wp_not_installed definition.

as you see function is checking if your site is installed by calling function from WordPress core is_blog_installed.

is_blog_installed definition.

It is hard to tell what is happening exactly with your site but I would try to debug this two functions.

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