When that warning shows up, you can open the Quick-Fix menu on the warning (Ctrl+1) and select
Ignore this warning
This will add the comment on the version line, like :
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
<version>1.1.0.Final</version><!--$NO-MVN-MAN-VER$-->
</dependency>
Your problem is you manually added that comment on the wrong line.
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