So here are the steps I performed to get silk workbench running on tomcat

1)
Clone a repo
git clone git@git.assembla.com:silk.git

2)
Make a new branch
git branch experiment

git checkout experiment

git status

here no changes - all files are as in the repo

the folder structure

silk
|
+silk2
|
+doc
+silk-jena
+silk-singlemachine
+silk-learning
+silk-workbench
+silk-core
+silk-mapreduce
+target
+silk-evaluation
+silk-server
+pom.xml


3) build required jars
now cd silk/silk2

mvn clean install

4) Edit files
cd silk-workbench/silk-workbench-webapp/

edit src/main/webapp/WEB-INF/web.xml comment out line for jetty uncomment line for tomcat

...
<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class><!-- Tomcat -->
<!--<servlet-class>org.eclipse.jetty.servlet.DefaultServlet</servlet-class>--><!-- Jetty -->
...

edit src/main/scala/de/fuberlin/wiwiss/silk/workbench/lift/Main.scala
comment out everything jetty related

package de.fuberlin.wiwiss.silk.workbench.lift

//import org.eclipse.jetty.server.Server
//import org.eclipse.jetty.webapp.WebAppContext

/**
 * Starts the Workbench.
 */
object Main {
  def main(args : Array[String]) {
    /*
    val server = new Server(8080)
    val webapp = new WebAppContext();
    webapp.setContextPath("/");
    val protectionDomain = Main.getClass.getProtectionDomain
    val location = protectionDomain.getCodeSource.getLocation.toExternalForm
    webapp.setWar(location);
    server.setHandler(webapp);

    server.start()
    */
  }
}

edit pom.xml find and comment out jetty dependencies

...
<!-- 
    <dependency>
      <groupId>org.eclipse.jetty</groupId>
      <artifactId>jetty-server</artifactId>
      <version>7.4.5.v20110725</version>
    </dependency>
    <dependency>
      <groupId>org.eclipse.s</groupId>
      <artifactId>jetty-webapp</artifactId>
      <version>7.4.5.v20110725</version>
    </dependency>
    <dependency>
      <groupId>org.eclipse.jetty</groupId>
      <artifactId>jetty-continuation</artifactId>
      <version>7.4.5.v20110725</version>
    </dependency>
     -->
....

5) buil the war
Make sure you are in silk-workbench/silk-workbench-webapp

mvn war:war

6) prepare tomcat
as the silk all over the place use "user.home" system variable
overwrite the user.home by modifying /etc/default/tomcat6

JAVA_OPTS="${JAVA_OPTS} -Duser.home=/home/sindice/silk"

where /home/sindice/silk is the directory where tomcat user can write

7) copy the generated war into webapps
cp target/silk-workbench-webapp-2.5.war $CATALINA_HOME/webapps/workbench.war

Done
Now you should see workbench running at http://example.com:8080/workbench

Note: it did not worked when deployed in different context then "workbench"
when I tried deploy it at http://example.com:8080/silk some ajax calls where broken (hardcoded "workbench" in url )
See
http://www.assembla.com/spaces/silk/tickets/242-hardcoded-ajax-urls

Richard tried Silk 2.5.2 on Tomcat 7.0.26 and it seemed to just work. On Tomcat 6 it does not.