Ok thanks for that interesting piece of software, I did run it and it detected nothing. The only extensions I use are Adguard, 1Password and Ghostery which have all been there for a long time. Not a big fan of extensions, I don't have any toolbar stuff other than standard Safari, and I remove all cookies and other databases usually twice a day.
Is there a folder you can suggest that I can look for the two databases listed above?
Also I will note that for at least the past 6 months I have noticed that deleting all website data, usually needs two deletions the first deletes cookies and then sometimes it reloads databases and caches which are cleared on the second deletion.
It is only very recently that the eBay.com cache which always cleared, began to reload immediately, and the new one search engine land, began very soon after. So that leads me to believe that some tool has recently been developed that can do this as it's just too much of a coincidence that these two should begin doing this within a very short time of each other.
EDIT:
Ok more info, I signed into my otherwise blank testing account opened up safari and deleted all cookies and caches. Nothing reloaded. Then I went to the searchengineland website deleted all stuff again, and the SEL cache returned. Opened up eBay.com.au deleted all caches again and only SEL returned, eBay.com.au cache did not return. Then I signed into eBay and as per my other account both the SEL and the eBay caches returned with no tabs open.
So this to me definitely looks like some new way to exploit some sort of vulnerability in Safari. It would appear that SEL is using it for all visitors so that once you have visited you'll always have their cache on your machine, however eBay appears to only use this exploit once you have signed in to your account, even though it is apparent that they could do that same as SEL which I obviously have not signed into.
I was wondering if you could check this out yourself and visit searchengineland and see if it is able to install a permanent cache on your computer. If so does this sound like a safari exploit? What is particularly bothersome is that because it reloads a cache file on your machine even when there are no tabs open the question remains that is it reloading a blank file or is it reloading a copied file so that you can never delete it?
I have just checked and the behaviour is also on eBay.com as well as .com.au once you have signed into your eBay account.
EDIT: 2
Ok the problem is happening in the ~/Library/Safari folder it is spread across Local Storage and Databases folders. Emptying the cache for the second time does seem to get rid of a lot of stuff but other items remain that are responsible for rebuilding it immediately.