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I'm using drush site-install for my initial site, and everything works great, but when I go to try create another site (using table prefixes so I can use the same database), drush attempts to drop and recreate the database, so I loose all the table from my first site. I know how to target drush to a particular subsite, but I'm not sure how to tell the drush site-install command not to drop the database tables.

Is there a better way to do this if I want to setup a initial site with 2 additional sites?

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Drush has very limited support for table prefixes; site-install is just one of the ways that Drush can fail. sql-sync has similar problems. It would take a lot of work to fully support table prefixes everywhere; it is best and safest to just use multiple databases when using Drush.

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