Answering my own question, I found I had to add the following to my 
gradle.properties to avoid gradle from picking up anything from my 
extensions folders:

systemProp.java.library.path=""
systemProp.java.ext.dirs=""


Also to note, this problem looks like it was specific to gradle and not Android 
Studio. 


Thanks,

steven


On Friday, September 18, 2015 at 11:20:48 AM UTC-4, Steven Yi wrote:
>
> Hi All,
>
> I've recently migrated a project from Eclipse to Android Studio (1.3.2). 
>  The application builds correctly and runs on the device.  However, one 
> thing I'm having a problem with is that the compiled application looks like 
> it it somehow packaging into the application classes from a Jar on my 
> system classpath, instead of the versions from the library module I have in 
> use.  If I remove the jar from the system classpath, the correct classes 
> from the library module are used. 
>
> Some background: the library module provides a native library + Java class 
> files.  This is an Android-specific version of a library that we also have 
> a desktop version for.  The desktop version may or may not be installed 
> into the user's system classpath.  Supporting the desktop version's 
> presence in the system classpath is a requirement for us.
>
> I have not figured out yet where in the build process that the desktop 
> version of the library is getting included.  It seems from using javap with 
> class files from the AAR generated in the library module that it is the 
> correct version there.  I am assuming there is something going on with the 
> application assembly process, but I have not investigated this aspect of 
> gradle and Android Studio yet.  
>
> If anyone has any suggestions or advice (or is this a known bug?), I would 
> appreciate it very much.
>
> Thanks!
> steven
>

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