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Please share a complete (at best executable) example, this snippet shows nothing that is directly relatable to Tycho and behavior obviously depends on the used version of Tycho and other plugins.
It's a simple parser bug. The <!-- ... --> gets confused by the internal < ... > allowing at least the <source-java-version>1.5</source-java-version> to be processed.
The following lines in pom.xml
<!--executionEnvironment>J2SE-1.5</executionEnvironment>
<source-java-version>1.5</source-java-version>
<target-java-version>${source-java-version}</target-java-version-->
caused a build to fail with 1.5 no longer supported. Changing to 1.8 within the comments and everything is ok.
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