Moved to maven to manage dependencies, which means moving away from
iText, and (for now) breaking the j3d stuff.
Serial IDs for servlets.
Remove ProteinServlet as it seems like a duplicate of DiagramServlet.
Clean up the DiagramServlet.
Move to default maven directory layout, and use jetty plugin.
Classpath changes.
Remove explicit src/test directories from pom.
Move the web.xml to the maven default dir.
Fix the servlet definitions in web.xml file.
Move the static content to the webapp dir.
Remove old web dir.
Force maven to use the right jre/compiler.
Put Terminii into the protein converter.
Add orientation to the converter, and put a test file in webapps.
Fixing bugs in the find files.
Test case for reading tops files.
Use a proper tops file, as created by the class.
Use the real path in the cartoon servlet.
Split the FindFilesServlet into a find and a summary action.
Add settings folder to gitignore.