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This is apktool related problem - when apktool can't detect the right package ID if apk uses 2 or more frameworks to decode resources (like MiuiFramework uses 1 and 8 packages).
So I've fixed this bug and fixed jbart2a will be released today.
Following error appears after decompile, compile and decompile the MiuiFramework.apk again:
[23.01.2015 13:43:24] I: **** Decompiling MiuiFramework.apk ****
[23.01.2015 13:43:24] I: Loading resource table...
[23.01.2015 13:43:24] I: Decoding AndroidManifest.xml with resources...
[23.01.2015 13:43:24] I: Loading resource table from file: D:\Xiaomi\MIUI\jBART\data\frameworks\1.apk
[23.01.2015 13:43:25] I: Loading resource table from file: D:\Xiaomi\MIUI\jBART\data\frameworks\10.apk
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=theme, value=0x080d0051
[23.01.2015 13:43:25] I: Regular manifest package...
[23.01.2015 13:43:25] I: Decoding file-resources...
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d0058
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d0058
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d00b6
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=background, value=0x080202b4
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d00b6
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d000d
[23.01.2015 13:43:25] W: Could not decode attr value, using undecoded value instead: ns=android, name=textAppearance, value=0x080d0058
[23.01.2015 13:43:26] I: Decoding values / XMLs...
[23.01.2015 13:43:26] S: pro.burgerz.bart.core.exceptions.DecompileException: c.a.a.e: resource spec: 0x080d0018
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