Not able to build project if the Library Base Path is different than ext/

I have changed the Library Base Path to 'resources/js/ext/'

Whenever I try to build my project it keeps complaning that it couldnt find ext-theme-neptune.

It only worked after I made a copy of resoruces/js/ext to ext/

I've also noticed that even though I changed the Base Path, a lot of the internal architect files (.sencha folder) still point the path to ext/

Bootstrap.js also had the paths set to the wrong location.

Ps: I've changed the Base Path at the beginning of the project, before I even added the Viewport and did the first save.

* Running Sencha Architect 3 for OSX version 3.0.4.1386