Why is maven-war-plugin failing for web.xml missing if I configured it not to fail on missing web.xml?

This should work:

<plugins>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-war-plugin</artifactId>
            <configuration>
                <failOnMissingWebXml>false</failOnMissingWebXml>
            </configuration>
            <executions>
                <execution>
                    <id>prepare-war</id>
                    <phase>prepare-package</phase>
                    <configuration>
                        <archiveClasses>false</archiveClasses>
                        <archive>
                            <manifest>
                                <addClasspath>true</addClasspath>
                                <classpathPrefix />
                            </manifest>
                            <manifestEntries>
                                <Implementation-Build>${build.number}</Implementation-Build>
                                <Implementation-Title>${project.name}</Implementation-Title>
                                <Built-By>${user.name}</Built-By>
                                <Built-OS>${os.name}</Built-OS>
                                <Build-Date>${build.date}</Build-Date>
                            </manifestEntries>
                        </archive>
                        <webResources>
                            <resource>
                                <!-- this is relative to the pom.xml directory -->
                                <directory>./target/dist</directory>
                            </resource>
                        </webResources>
                    </configuration>
                </execution>
            </executions>
        </plugin>

Please notice that the <failOnMissingWebXml>false</failOnMissingWebXml> section has been moved up to the plugin configuration rather than the execution.

The execution ID in the POM is prepare-war. Maven runs its own default execution of the war plugin for projects with packing type war. The default execution has ID default-war. As the POM is currently configured, the war goal is running twice.

If you look at the error message:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.4:war (default-war) on project com.specktro.orchid.operations.portal.frontend: Error assembling WAR: webxml attribute is required (or pre-existing WEB-INF/web.xml if executing in update mode) -> [Help 1]

You may see the execution ID that fails in parenthesis (default-war). If you change the execution ID to default-war your problem will go away, AND you will no longer have two executions of the war goal running.