In Unity 5, how do I replace files instead of appending "1" and duplicating?

I'm running into the same issue. Having the filenames have " 1" after them makes it much more difficult to update a .unitypackage that I'm already using.

I tried importing "unitypackage" in 3 different ways:

-Directly click on it while project is opened

-Through assets store

-Project view => R$$anonymous$$B => Import package => Custom package

I couldn't replicate the issue with any of those methods above^. None of the preference assets checkboxes could cause this issue either.

Have you done anything else to your Unity editor after installation? Some plugins, extensions?

No, this was a fresh install of Unity. I tried by double clicking on the package while my project was open, and also doing Assets > Import Package > Custom Package. You were using Unity 5 @DoTA_$$anonymous$$A$$anonymous$$I$$anonymous$$ADzE ? I'm not using prime 31, but I see them making note of this same issue in their release notes (search for "space 1" in there).

One thing to note was that the packages had to be different in some way to cause the duplicate files. If I import the exact same .unitypackage twice, then there are no files to import. But if I have version 1 of a .unitypackage and version 2 of a .unitypackage, then the 1 behavior happens. It happens for all files in the package, regardless of whether or not a particular file changed between version 1 and 2 of the plugin

Tried with different package versions, different locations and even renamed package to something else. Still can't replicate your issue. And yes I'm using Unity 5 (5.0.1f1) everything was also fine on 5.0.0f4 version as well.