So I've added remote server to PhpStorm and I can change files there. But if I delete files they disappear only from my computer not on the server.
How to delete files from remote server using PhpStorm?
To manually delete files from remote location -- use Remote Host tool window (or Tools | Deployment | Browse Remote Host
if it's not visible) -- navigate and delete any file(s) you want.
For keeping your remote host in sync with local (i.e. to delete remote file as soon as local gets deleted as well) you need to enable automatic upload in Settings | Deployment | Options
, in particular:
Obviously, you need to configure all those options as most suitable to your workflow.