We have a multi-module project with the following structure:

batch.jar (created using Spring boot)
--persistenceContext.xml (containing definition SqlSessionFactoryBean - see bellow)
--package1/package2/Mapper1.xml (specific mapper for batch module)
--package1/package2/Mapper1.java (specific mapper for batch module)
--lib/persistence-module.jar
--lib/persistence-module.jar/package3/package4/Mapper2.xml (common mapper re-used by multiple modules)
--lib/persistence-module.jar/package3/package4/Mapper2.java (common mapper re-used by multiple modules)
--lib/persistence-module.jar/package3/package5/typehandler/DateTimeHandler.java (common typehandler re-used by multiple modules)

relevant parts of the persistenceContext.xml (placed in the OUTER jar file):

<!-- define the SqlSessionFactory -->
<bean id="sqlSessionFactory" class="org.mybatis.spring.SqlSessionFactoryBean">
  <property name="dataSource" ref="dataSource" />
  <property name="typeHandlersPackage" value="package3.package5.typehandler" />
</bean>

<!-- scan for mappers and let them be autowired -->
<bean class="org.mybatis.spring.mapper.MapperScannerConfigurer">
  <property name="basePackage" value="package1.package2, package3.package4" />
</bean>

The mapper scanning works without any problems (even for the Mapper2, which is placed in the inner jar file).
But typehandler scanning does not work correctly - the custom type handler DateTimeHandler.java is not found by myBatis in this configuration. I think the problem is on line 202 in org.apache.ibatis.io.DefaultVFS.java:

url = new URL(url.getFile());

This causes the URL in the form of "jar:file:batch.jar!/lib/persistence-module.jar/package3/package5/typehandler" is transformed to "file:batch.jar!/lib/persistence-module.jar/package3/package5/typehandler" and Exception is thrown on attempt to read from this URL on line 288 (isJar method).

Workaround I had to use was to duplicate the DateTimeHandler.java and put it to the outer jar (batch.jar) as well + change the spring context so now the scanned type handler package is the one in the outer jar. But this solution is of course not ideal and I definitely consider this as a bug (especially because rest of the mybatis configuration - i.e. the mapper scanning is working normally even for the mappers placed in the INNER jar).
Also I think the "swallowing" of the Exception in DefaultVFS.isJar() without any logging is not very good and it took me some time debugging the sources before finding the cause of this problem (and obviously the comment "Failure to read the stream means this is not a JAR" is not correct).