1. Through a simple search option
2. Download verification

First, let me register directories that will not be shared within client. It might be Tools:Options:Sharing under the "Shared Extensions" -- a 3rd section "Non-shared directories for download verification and search filtering."

1. Add a simple check-box over the search button. When it is checked, any file matches between search results (name+size or whatever metrics you use) and shared + non-shared files will not be displayed in the search results window.

Important: The check-box must toggle the search view on-the-fly. Don't make me repeat a search to change the box.

2. When a download is started and a requested download matches an existing file (anywhere in shared or non-shared file directories) a pop-up with details will appear:

You have ./yourdir/yourfile size date etc.
do you wish to download newfilename size date etc.
Yes / No / Overwrite

I cannot tell you how much time this would save me.

Thanks!