Cannot rebuild decoded apk (InvalidTryException: Multiple overlapping catches for ClassNotFoundException)

[iBotPeaches]

Original issue 675 created by shirokuroneko on 2014-08-26T21:46:31.000Z:

What steps will reproduce the problem?

1. apktool d ly.secret.android.apk
2. apktool b ly.secret.android.apk

What is the expected output? What do you see instead?
Decoding works and since there were no changes it should be able to rebuild the apk again. However, it fails with this error:

I: Using Apktool 2.0.0-3d2e93-SNAPSHOT on secret
I: Checking whether sources has changed...
I: Smaling smali folder into classes.dex...
Exception in thread "main" org.jf.dexlib2.writer.util.TryListBuilder$InvalidTryException: Multiple overlapping catches for Ljava/lang/ClassNotFoundException; with different handlers
at org.jf.dexlib2.writer.util.TryListBuilder$MutableTryBlock.addHandler(TryListBuilder.java:180)
at org.jf.dexlib2.writer.util.TryListBuilder.addHandler(TryListBuilder.java:311)
at org.jf.dexlib2.writer.util.TryListBuilder.massageTryBlocks(TryListBuilder.java:69)
at org.jf.dexlib2.writer.DexWriter.writeCodeItem(DexWriter.java:883)
at org.jf.dexlib2.writer.DexWriter.writeDebugAndCodeItems(DexWriter.java:759)
at org.jf.dexlib2.writer.DexWriter.writeTo(DexWriter.java:214)
at org.jf.dexlib2.writer.DexWriter.writeTo(DexWriter.java:192)
at brut.androlib.src.SmaliBuilder.build(SmaliBuilder.java:57)
at brut.androlib.src.SmaliBuilder.build(SmaliBuilder.java:41)
at brut.androlib.Androlib.buildSourcesSmali(Androlib.java:358)
at brut.androlib.Androlib.buildSources(Androlib.java:298)
at brut.androlib.Androlib.build(Androlib.java:284)
at brut.androlib.Androlib.build(Androlib.java:258)
at brut.apktool.Main.cmdBuild(Main.java:240)
at brut.apktool.Main.main(Main.java:89)

What version of the product are you using? On what operating system?
apktool version: top of tree snapshot 3d2e93 (26/08/2014). Built following the wiki instructions.
java version "1.7.0_65"
Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
Running in Mac OS X 10.9.4

Please provide any additional information below.
Play store link to the apk: https://play.google.com/store/apps/details?id=ly.secret.android

[iBotPeaches]

Comment #1 originally posted by connor.tumbleson on 2014-08-27T18:17:42.000Z:

This is an upstream bug with smali: https://code.google.com/p/smali/source/detail?r=0d8418ff1f253471dc5f579ec5b4976c08649a09

Once merged the compilation completes but fails on an aapt problem.

[iBotPeaches]

Comment #2 originally posted by connor.tumbleson on 2014-09-24T12:23:47.000Z:

394bb25

Fixed via cherry-pick of smali.