I have solved this problem by repackaging
yuicompressor, rhino and tap-yuicompressor into a single .jar file
using jarjar, which solves all problems.
I don't think there is a 'clean' solution.

---------------
Combine yucompressor-2.4.6 and rhino-1.6R7 into src file (via jar)
$ mkdir work; cd work
$ jar xf ~/.m2/repository/rhino/js/1.6R7/js-1.6R7.jar
$ jar xf 
~/.m2/repository/com/yahoo/platform/yui/yuicompressor/2.4.6/yuicompressor-2.4.6.jar
 
$ jar xf 
~/.m2/repository/org/apache/tapestry/tapestry-yuicompressor/5.3.2/tapestry-yuicompressor-5.3.2.jar
$ jar cfm ../yuic.jar META-INF/MANIFEST.MF .

Using instructions in 
http://yuilibrary.com/projects/yuicompressor/ticket/2527981
to generate yuicompressor and upload it to the BAW repo
$ java -jar jarjar-1.2.jar process yui-rules.txt yuic.jar 
yuicompressor-2.4.6-cust-tap-5.3.2.jar

$ mvn deploy:deploy-file -DgroupId=com.yahoo.platform.yui 
-DartifactId=yuicompressor -Dversion=2.4.6-cust-tap-5.3.2 -DgeneratePom=true 
-Dpackaging=jar -Dfile=yuicompressor-2.4.6-cust-tap-5.3.2.jar 
-DrepositoryId=repo -Durl=file://flowlogix-m2
-------------------------

----- yui-rules.txt ----------------------
rule jargs.gnu.** com.yahoo.platform.yui.@0 
rule org.mozilla.** com.yahoo.platform.yui.@0 
keep com.yahoo.** 
keep org.apache.**
-----------------------------------

On Jul 4, 2012, at 4:48 AM, Felix Gonschorek wrote:

> howard,
> 
> i encountered problems with yuicompressor too (in the rc5 release i
> think). i deactivated the yuicompressor tap5 module to fix it. the
> problem for me was this:
> 
> http://yuilibrary.com/projects/yuicompressor/ticket/2528056
> 
> the yuicompressor has its own version of the rhino classes, but in the
> same package hierachy. i have my own (newer)  rhino dependency in the
> classpath. when the yuicompressor rhino classes gets loaded first, my
> application starts to massively throw exceptions.
> 
> maybe this helps narrowing down things.
> 
> felix
> 
> 
> Am 03.07.2012 18:16, schrieb Howard Lewis Ship:
>> I've just released Tapestry 5.3.4-rc-9.
>> 
>> The only difference from rc-8 is that the POM for
>> tapestry-yuicompressor correctly identifies the repository one of its
>> dependencies comes from (that is not in the Maven central repository).
>> 
>> However, may people (including myself) are having issues with
>> yuicompressor in running applications; I'm still trying to get to the
>> core of it, my working theory is some conflict between the patched
>> version of Rhino (the JavaScript engine) inside the yuicompressor
>> library, and the version of Rhino that is packaged with JDK 1.6 and
>> up.
>> 
> 
> 
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