A bug report regarding the editing of resources that are located in a zip file. When you edit a file inside a zipfile and send the build to SalesForce, it zip's the files and uploads the resource. Somehow in the latest version (16.2.4) it will zip the root folder as well, causing the folder order to be wrong.

Original file, named ic.zip:

Zipfile -> css (folder)   -> files

               js (folder)      -> files

               fonts (folder) -> files

When uploading with the latest version the following happens:

Zipfile -> Resources (folder) -> ic (folder) ->  css (folder)   -> files

                                                                       js (folder)      -> files

                                                                       fonts (folder) -> files

It seems to be taking the root folders from the project folder in regard to path name while uploading.

[attachment=15:Schermafdruk 2015-04-17 11.57.19.png]

In this picture Left is the original file, Right is the file uploaded by Welkin Suite 16.2.4

[Edit]

It seems that after deleting the old project and pulling a fresh one, you get a "stacking" directory, it places the all of the files in another level of Resources/ic folders. So it gets deeper and deeper!