I have collected all sorts of rubbish that i would like to clean up on my server. Of course doing a backup first but has anyone been brave enough to delete all the files on their server for a website and re-upload from Elements to clean it up?
As long as you have a backup there should be no worry about doing this, especially if your entire site is in Elements, just do a “Re-Publish All Files” 
I do this all the time with no issues.
A little spring cleaning is highly recommended, just make sure you have that backup beforehand. 
Hi @dan and @differentdan Couldn’t a command be added to clear the site before a complete re-upload?
An option attached to “Re-Publish all files” that would delete everything before re-uploading.
I don’t understand the point of working with Elements, which seems to offer everything we need, such as .htaccess, robets.txt, etc., and yet still having to regularly perform manual cleanup on the server, for example, to remove .md files or delete files before re-uploading.
Publishing in RapidWeaver has always been non-destructive, meaning the app will overwrite a file if it has the same filename (e.g. index.php to index.php), however it will not delete files/folders off of the server. This is deliberate as deleting files/folders off of people’s web server is something they should do manually, not something the app should handle. I can imagine the support tickets we would get along the lines of “Your app deleted a very important file off of my hosting account!”, not something we really want to deal with.
Logging into your web hosting control panel to delete files/folders should be a trivial task. You can also use an FTP client as well, such as Cyberduck, which is free.