AEM Apps builds upon the existing ContentSync framework. See http://docs.adobe.com/docs/en/aem/6-0/develop/mobile/contentsync.html
ContentSync is used to export the content from AEM into a zip which contains the static files representing your app (content and resources)
If you use libraries or more and do not see them once exported from AEM you should review your ContentSyncconfiguration(s). The shell configuration exports several clientlibs as seen at https://github.com/blefebvre/aem-phonegap-starter-kit/tree/master/content/src/main/content/jcr_root/.... As Anthony mentioned earlier there are options on how to get you libraries in.
Looking at Bruce's repo there are several ContentSync configs (searching for node type of contentsync/config over repo);
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\en\_jcr_content\pge-app\app-config\.content.xml(9): sling:resourceType="contentsync/config"
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\en\_jcr_content\pge-app\app-config-dev\.content.xml(9): sling:resourceType="contentsync/config"
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\shell\_jcr_content\pge-app\app-config\.content.xml(9): sling:resourceType="contentsync/config"
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\shell\_jcr_content\pge-app\app-config-dev\.content.xml(9): sling:resourceType="contentsync/config"
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\shell\_jcr_content\pge-app\app_name_placeholder\.content.xml(9): sling:resourceType="contentsync/config"
aem-phonegap-starter-kit-master\content\src\main\content\jcr_root\content\phonegap\app_name_placeholder\shell\_jcr_content\pge-app\app_name_placeholder-dev\.content.xml(9): sling:resourceType="contentsync/config"
Note 6 configs.
There are main 2 packages contributing content; en and shell.
Each has a complimentary dev copy of the config. (dev to latest JCR changes, main/production to manage production app updates).
Shell has an additional aggregate package (also has a complimentary dev copy) that represents the full app. This config is the one that pull in all other content packages into a single consolidated export (in this case en + shell).
You may have more package then you choose to include in the initial app. Package not included in the initial app can be delivered to the app as an update as needed as they would not be part of initial app.
John