outputDirectory is not honored as it should, but valuated to destDir.

I'm not sure what it is that you want.

The alias="destDir" indicates that this parameter has been renamed from "destDir" to "outputDirectory". The alias makes it possible to keep the old name of the parameter for backwards compatibility.

The expression="$

" part means that if you want to specify this parameter on the command line you should use the syntax:
-DdestDir=my/chosen/path

What I want is to put the directory where are generated the javadocs outside the target/site directory and none of the outpuDirectory ot destDist parameters let me do so. It is like the kink option that always produces an ablsolute file while it should be relative if it has beeing specified as relative.

As exemple

with
<destDir>api/als</destDir>
<detectLinks>true</detectLinks>
<links>
<link>../asn</link>
<link>../ugn</link>
</links>

the plugin generates link as below

D:/OSI/iso.itu.osi.als/target/site/apidocs/api/als\../asn/package-list

which is not what I am expecting since the asn/package-list will never located under the target site/apidocs/als directory...

IMHO, all path should be relative to the expressed outputDirectory where anyone can put its own link referrals.

With this configuration
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.7</version>
<!--
<executions>
<execution>
<id>aggregate</id>
<goals>
<goal>aggregate</goal>
</goals>
<phase>site</phase>
</execution>
</executions>
-->
<configuration>
<outputDirectory>$

</outputDirectory>
<destDir>api</destDir>
</configuration>
</plugin>

then outputDir is totally ignored while destDir redirects to target/site/apidocs/api

as view in the log
Constructing Javadoc information...
Standard Doclet version 1.6.0_24
Building tree for all the packages and classes...
Generating C:/Documents and Settings/C59FAND/Mes documents/g37idn/asm/target/site/apidocs/api\test/\Edition.html...

With such configuration, i am expecting that the javadoc be produced in
Generating C:/Documents and Settings/C59FAND/Mes documents/g37idn/asm/api

Happens also on Ubuntu:
Apache Maven 3.0.3 (r1075438; 2011-02-28 18:31:09+0100)
Java version: 1.6.0_26, vendor: Sun Microsystems Inc.
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-32-generic", arch: "amd64", family: "unix"

The workaround (or the right way to do it) is include also

<reportOutputDirectory>$

</reportOutputDirectory>

when deploying the site, you'll get what you expect
it's normal that the site has this "problem" at build time