Can you provide meaningful prefixes for conflicting files? When you detect a file name conflict, construct a distinguishing prefix for each conflicting file from the difference in tags on the conflicting files. (If all the tags are the same, then fallback to a synthetic prefix or overwrite the file or error out or whatever.)
For example, let's say you have /photos/london/DSCN0001.JPG and /photos/vienna/DSCN0001.JPG, where "london" and "vienna" are both included in "europe". This could yield paths like /photos/europe/london:DSCN0001.JPG and /photos/europe/vienna:DSCN0001.JPG.
The big trouble here (and, if I understand, with what you're suggesting as well) is that changing the name or tags of one file can alter the path to another as a side effect. So if I started with just /photos/vienna/DSCN0001.JPG, I might reference it as /photos/europe/DSCN0001.JPG somewhere. But when I go back and add /photos/london/DSCN0001.JPG, my reference to the photo of Vienna breaks because its name is no longer unique. As TeMPOral points out, this is a general class of problems afflicting a system like this.
When you create a file "DSCN0001.JPG", it receive a prefix, even if it's not conflicting, becoming, lets say, "123_DSCN0001.JPG".
But both you and your software (say: a filemanager) are presuming the file is named "DSCN0001.JPG", not "123_DSCN0001.JPG". To solve that, Tagsistant 0.4 provides an aliasing layer that maps the original name to the prefixed one.
It's still something under development, so both the idea and the implementation can change. For example: how long should an alias exists? Just after the first access? Up to an extimated expiration time?
I'm oriented to the latter solution. Being aliases implemented as an SQL table, adding a expiration column and a garbage collecting thread should be all that is needed.
Of course, using expiring aliases is just like postponing the problem. But, in my opinion, Tagsistant is primary a personal tool, nothing that automated procedures or batches are supposed to rely on. I hope that, in this perspective, the alias workaround is an acceptable compromise.
For example, let's say you have /photos/london/DSCN0001.JPG and /photos/vienna/DSCN0001.JPG, where "london" and "vienna" are both included in "europe". This could yield paths like /photos/europe/london:DSCN0001.JPG and /photos/europe/vienna:DSCN0001.JPG.
The big trouble here (and, if I understand, with what you're suggesting as well) is that changing the name or tags of one file can alter the path to another as a side effect. So if I started with just /photos/vienna/DSCN0001.JPG, I might reference it as /photos/europe/DSCN0001.JPG somewhere. But when I go back and add /photos/london/DSCN0001.JPG, my reference to the photo of Vienna breaks because its name is no longer unique. As TeMPOral points out, this is a general class of problems afflicting a system like this.