Regarding the file scanner, this means that your host is too slow or too restrictive for the file scanner to work. Sorry, I can't do anything about it yet :( I am going to add more fine-tuning options in the future, just like Akeeba Backup has (it's the same engine, actually), which could probably allow us to work around hosts like yours.
Regarding the search module, this is a completely unrelated issue. Please start a new ticket and tell me if it's the core search box or a third party module (if so, which one). Also tell me what exactly happens. "It doesn't work" may mean "I type something and there is no auto-complete", "I hit the ENTER key and nothing happens", "I get such and such error message when submitting the search query" and so on. I am not in front of your computer, I do not know the domain name of your site and I'm a very, very lousy psychic. You have to be my eyes. If you don't give me the full picture, I will be probably wasting your time with advice inapplicable to your issue. Help me help you, please :)
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
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