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!

Check out the latest 3.9.8 beta. It contains extra icons that are in place of the stars that indicate whether a search result is already downloading, is stored in an incomplete file (but not currently downloading) or already in your saved or shared folder. (Matching for files downloading, incomplete or in the shared folder are all lookups of the hash of the file. Matching for the saved folder [regardless of whether or not it is shared] is done by the hash of the file OR the file name.)