m2e-wtp can't be disabled for the moment at the workspace level. Please open a feature request at
As a workaround, you can tell m2e to ignore the m2e-wtp configurator(s) directly in your pom.
<profiles>
<profile>
<id>m2e</id>
<!-- This profile is only activated when building in Eclipse with m2e -->
<activation>
<property>
<name>m2e.version</name>
</property>
</activation>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<versionRange>[2.0.1,)</versionRange>
<goals>
<goal>war</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</profile>
</profiles>