Ext JS 4.1.3 アプリケーション用に、'app' という名前のカスタム フォルダーを使用する必要があります。Sencha のドキュメントでは、このフォルダ名が「appFolder」と呼ばれる設定可能な値であることは明らかです。
環境: Ext JS 4.1.3 Sencha Cmd 3.1.2.342 Ruby 1.9
私が取った手順：
sencha generate workspace C:\temp\workspace
sencha -sdk C:\tools\extjs4.1.3 generate app common C:\temp\workspace\common
cd C:\temp\workspace\common
sencha app build
SUCCESSFUL
app.js を編集し、appFolder: 'custom': を設定しました。
Ext.application({
appFolder: 'custom' ...
また、「C:\temp\workspace\common\app」フォルダーの名前を「C:\temp\workspace\common\custom」に変更しました
sencha app build.
[ERR] def was null
[ERR] failed to find meta class definition for name common.controller.Main
[ERR] def was null
[ERR] failed to find meta class definition for name common.view.Viewport
[ERR] C2008: Requirement had no matching files (common.view.Viewport) -- unknown
-file:-1
[ERR] Error executing page compilation Failed to find any files for C:\TEMP\workspace\common\app.js::ApplicationAutoDependency::common.view.Viewport
[ERR]
[ERR] BUILD FAILED
[ERR] com.sencha.exceptions.ExBuild: com.sencha.exceptions.ExBuild: Failed to find any files for C:\TEMP\workspace\common\app.js::ApplicationAutoDependency::common.view.Viewport
[ERR]
[ERR] Total time: 6 seconds
[ERR] The following error occurred while executing this line:
C:\TEMP\workspace\common\.sencha\app\build-impl.xml:408: The following error occurred while executing this line:
C:\TEMP\workspace\common\.sencha\app\build-impl.xml:381: com.sencha.exceptions.ExBuild: com.sencha.exceptions.ExBuild: Failed to find any files for C:\TEMP\workspace\common\app.js::ApplicationAutoDependency::common.view.Viewport