1. I am not sure I am right but did you check the options? You can either choose to only work with the MEDIA or/and the FILESYSTEM. Does this help?
2. Is it really an issue? Do you really need to go to the page 8 directly? Same it’s more code to add and the current way is quite neat (in my opinion) and suffice. You can also change the &paged=1 directly at the top with the number you like, but do you really have to do that kind of operation often?
3. Yes it is but I like it the way it is. Usually people will go away from the page or the computer while this is being done. If they see the refreshed page maybe they will forget that they pushed that button. Writing the message and ask the user to refresh the page makes sure he knows that the operation was performed. I could display a message after the refresh too but it’s much more code to write and to test so I prefer not 🙂
1 – are you saying that “Media (DB entry) not found” issue is related only to “Scan Media” in the settings and “Not used files” issue is related only to “Scan Files”? And there are no other possible issues? That was not very obvious to me. But if that’s the case, this will work, too. I would only add in a little explanation, something like “The Media Library will be scanned for Media (DB entry) not found issue)” and “The Uploads folder will be scanned for Not used files issue”. Alternatively you could scan for all the issues, but let the user decide what he wants to do with the results – filter out by the file name or by the issue. Because you already have the file name filter, I thought adding the “issue” filter would be more logical in this situation?
2 – not a big issue. There was a situation where I wanted to quickly scroll through the pages to check on an issue where I didn’t remember the filename. Otherwise I would use the file search function which serves same purpose.
3 – this is mainly for consistency, convenience and automation. I noticed many operations in WordPress use autorefresh. For example, you add the files to the library, you see the process, “crunching” and then you don’t see the button “please refresh to see the changes”, you see the library contents autorefreshed. However if this makes the code a lot more complicated, and you prefer simplicity over automation at this point, I can understand that.
Media (DB entry) not found is shown when a file is not used anywhere (content) AND not found in the Media Library either. This is part of the “Scan Files” since… “Scan Media” can be found in the Media Library as entries anyway 🙂
I don’t want to filter after the scan but I could think of the settings a bit differently and add conditions in order to tune-up the scanning. Not sure how to do that though, I don’t have enough feedback on this plugin at this point to really know what at the usage (except from you).