Migrating from meteor 1.2.1 to 1.3 or 1.4 - problem with local packages



I have an application based on meteor with angular where most of the implementation is in a local package.
This package worked just fine on Meteor 1.2.1 but when trying to use it in a new project based on Meteor or 1.3 things break.
The first problem I see is that the build process takes all the files it finds under the package directory instead of only the files I specify in package.js using api.addFiles(). That is, looking in .meteor/local/build/programs/web.browser/packages/.js I can see that all the files where included.

Why is that?
How can I solve the problem?
Do I have to remove any redundant file?