I have a similar issue.
I just upgraded from "Maven Integration for Eclipse 0.9.3.20080421-2352" to "0.9.4.20080603-0114"
Under both versions, my .classpath file has this for the resources :
<classpathentry excluding="**" kind="src" output="src/main/resources" path="src/main/resources"/>
<classpathentry excluding="**" kind="src" output="src/test/resources" path="src/test/resources"/>
Using 0.9.3, when launching via the "Java Application" launcher, my project launches fine, however in 0.9.4, my application is unable to load resources from the classpath (files under the src/main/resources/ folder)
for example :
Caused by: java.io.FileNotFoundException: class path resource [hibernate.cfg.xml] cannot be resolved to URL because it does not exist
at org.springframework.core.io.ClassPathResource.getURL(ClassPathResource.java:162)
at org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:603)
at org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:211)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1367)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1333)
... 66 more
I even tried resetting the launch target's classpath to default entries.
I can resolve this issue by removing th excluded="**" attribute in .classpath, and I originaly thought this was a bug until I noticed that 0.9.3 uses this too.
SO, I must be doing something wrong - however I havn't changed anything in my project, I've just upgraded the plugin.
Regards
Cameron
see the picure. You see that resources subfolders are excluded