[Android] dsixda:
I just tried out your ROM, and it deodexed fine. :P

Did you try the recommended option to deodex both folders at once, or did you just do the app folder??

I think the problem you saw was that it gave a warning when it tried to deodex it at the beginning (as you showed in the screenshot), but right after that the script used a 'brute force' method (which you didn't show in your screenshot) to deodex the file by trying out all the JAR files in the framework folder for a possible match. After a couple of tries it doedexed successfully..

If you wait for the deodex routine to finish then you will see whether there were real failures or not.. I'll update the deodexing routine anyway so that you don't see those (harmless) warnings for Clicker.odex, by defining android.test.runner.jar for it.

Here's the output I had seen originally.. as you can see, it deodexed successfully at the end:

NOW AT FILE 12 OF 115 IN system/app: Clicker.odex
Disassembling Clicker.odex ...
java -Xmx512m -jar baksmali.jar -d ../framework -x Clicker.odex

Error occured while loading boot class path files. Aborting.
org.jf.dexlib.Code.Analysis.ClassPath$ClassNotFoundException: Could not find superclass Landroid/test/InstrumentationTestRunner;
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.loadSuperclass(ClassPath.java:784)
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.<init>(ClassPath.java:668)
at org.jf.dexlib.Code.Analysis.ClassPath.loadClassDef(ClassPath.java:280)
at org.jf.dexlib.Code.Analysis.ClassPath.initClassPath(ClassPath.java:163)
at org.jf.dexlib.Code.Analysis.ClassPath.InitializeClassPathFromOdex(ClassPath.java:110)
at org.jf.baksmali.baksmali.disassembleDexFile(baksmali.java:96)
at org.jf.baksmali.main.main(main.java:278)
Error while loading class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner; from file Clicker.odex
Error while loading ClassPath class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner;

WARNING: Cannot deodex Clicker.odex

-> Using brute-force method to find the required class:

Trying dependency with am.jar ...
Disassembling Clicker.odex ...
java -Xmx512m -jar baksmali.jar -d ../framework -c :am.jar -x Clicker.odex

Error occured while loading boot class path files. Aborting.
org.jf.dexlib.Code.Analysis.ClassPath$ClassNotFoundException: Could not find superclass Landroid/test/InstrumentationTestRunner;
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.loadSuperclass(ClassPath.java:784)
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.<init>(ClassPath.java:668)
at org.jf.dexlib.Code.Analysis.ClassPath.loadClassDef(ClassPath.java:280)
at org.jf.dexlib.Code.Analysis.ClassPath.initClassPath(ClassPath.java:163)
at org.jf.dexlib.Code.Analysis.ClassPath.InitializeClassPathFromOdex(ClassPath.java:110)
at org.jf.baksmali.baksmali.disassembleDexFile(baksmali.java:96)
at org.jf.baksmali.main.main(main.java:278)
Error while loading class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner; from file Clicker.odex
Error while loading ClassPath class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner;

WARNING: Cannot deodex Clicker.odex
$
Trying dependency with android.policy.jar ...
Disassembling Clicker.odex ...
java -Xmx512m -jar baksmali.jar -d ../framework -c :android.policy.jar -x Clicker.odex

Error occured while loading boot class path files. Aborting.
org.jf.dexlib.Code.Analysis.ClassPath$ClassNotFoundException: Could not find superclass Landroid/test/InstrumentationTestRunner;
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.loadSuperclass(ClassPath.java:784)
at org.jf.dexlib.Code.Analysis.ClassPath$ClassDef.<init>(ClassPath.java:668)
at org.jf.dexlib.Code.Analysis.ClassPath.loadClassDef(ClassPath.java:280)
at org.jf.dexlib.Code.Analysis.ClassPath.initClassPath(ClassPath.java:163)
at org.jf.dexlib.Code.Analysis.ClassPath.InitializeClassPathFromOdex(ClassPath.java:110)
at org.jf.baksmali.baksmali.disassembleDexFile(baksmali.java:96)
at org.jf.baksmali.main.main(main.java:278)
Error while loading class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner; from file Clicker.odex
Error while loading ClassPath class Lcom/htc/android/htcime/misc/ClickerTests/ClickerTestRunner;

WARNING: Cannot deodex Clicker.odex

Trying dependency with android.test.runner.jar ...
Disassembling Clicker.odex ...
java -Xmx512m -jar baksmali.jar -d ../framework -c :android.test.runner.jar -x Clicker.odex
Assembling into classes.dex ...
java -Xmx512m -jar smali.jar -o classes.dex out
Found Clicker.apk
Removing Clicker.odex ...
Put classes.dex into Clicker.apk ...