Simply enough,

...
           <plugin>
               <artifactId>maven-site-plugin</artifactId>
               <configuration>
                   <siteDirectory>site</siteDirectory>
               </configuration>
           </plugin>
...

I doubt, however, that this is really what you're looking for. At risk of stating the obvious, you will be much happier in the long run if you can transition to the standard directory structure. By taking a half-and-half approach, you will most likely feel equivalent pain again when you decide you really should accept Maven's opinionated ways.

Dan Rollo wrote:
Does anybody know of a good place to put some free-form documentation files in the maven project/pom.xml?

I know the default location appears to be "src/site", but I overrode the default source location when creating our pom.xml (to minimize changes) to be "src". Therefore, stuffing docs into the actual source code tree would be confusing (at best).

I couldn't see where to configure an override for the site input in a pom.xml.

Our project pom overrides are:

...
    <build>
        <sourceDirectory>src</sourceDirectory>
        ...
        <testSourceDirectory>test</testSourceDirectory>
...


Thanks,
Dan

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