After altering the .mpk file to zip and extracting, altering a .js file inside and zipping the files back with a .mpk file extension results in the following error. Package 'C:\Users\User\Documents\Company\widgets\Widget1.mpk': Client module specifies file path 'Widget1/' that does not exist in the package. On unzipping the files again, they are in the exact structure when unzipping the original unchanged widget.
Are you using the built-in compress utility of Windows? Zip files created with this utility are known to cause issues like these. Do you run into the same issue when using for instance 7-Zip to create a widget package?