Eclipse maven multi module project issues

Most developers I know moved on to IntelliJ for just one reason: better support for development and reload/hot deployment of multi module maven projects and its resources. All of these problems keep happening in the case of nested/hierarchical multi module maven projects which is >90% of maven use cases:
1. Every time a multi module project is imported, sometimes there are both referenced libraries and maven dependencies in some projects. We have to manually remove referenced libraries from appearing. How can stop this from happening?
2. Changes made to resource updates are not always refreshed and require full clean, using eclipse:clean eclipse:eclipse commands and even a maven project refresh using Alt+F5? Why should we do this and not let Eclipse figure out what's wrong? Also, Eclipse updates to dependency projects are slow when fixing any compile time issues from dependencies.
3. Maven sometimes import dependency projects and its resources into its classpath and sometimes imports final artifact or jar from local repository as its dependency. This is a major problem just because jars excludes specific resources, say, from its src/main/resources. Is there a way in Maven to ask it to use resources of final artifact or exclude files that are not part of the its dependency packaging, typically excluded in the the dependent pom by <exclude>resource... without manually updating classpath?
4. When deploying a multi module project to an Eclipse Tomcat container, resources are not deployed randomly. Say a dependency src/main/resources has dep1-config.xml and you want to specify a custom file dep1-config.xml runtime, there is currently no way to say override from the main project being deployed or from custom folders added to classpath of project being deployed. Guess this is a problem with the container classloader and not really a maven issue.
5. There isn't a single multi module project deployment tutorial with best practices of managing classpath resources anywhere.
How hard is it to make a stable maven support just like IntelliJ?

Please do not use the maven-eclipse-plugin (mvn.eclipse:eclipse) and m2e simultaneously, they're not very compatible. Instead, when issues happen, clean your project in the m2e way, using the "Maven > Update configuration" context menus on your project(s).

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    jcshell: Error code: 6a80 (Wrong data)
    jcshell: Wrong response APDU: 6A80
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    jcshell: Wrong response APDU: 6A80
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