Looks like we can't reproduce the issue or there's a problem in the test case provided.
Compile and concatenate only app files with v126.96.36.199
but the minified file includes Ext files also. Is this a bug in .230 (MacOSX 10.6.8) or the command is wrong ?
sencha compile -classpath=app union -r -namespace MyAppNamespace and concat -yui minified.js
EDIT: hmmm, seems that this one gives the expected output:
sencha compile -classpath=app exclude -all and include -namespace MyApp and concat -yui minified.js