Does your skin declare that it has a custom js file?
For example, your skin.properties.xml file should have something like this:
<!-- dynamic js file -->
<property>
<name>scripts/base.js</name>
<value>scripts/base.jsi</value>
<description>standard scripts</description>
</property>
When the skin archive is being deployed, the files specified using *.jsi properties are processed to create the *.js files.
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