When jpa+seam project is created it model and action folders are <project_name>/src (when only seam model=<project_name>/src/main and action=<project_name>/src/hot). See SeamFacetAbstractInstallDelegate#copyFilesToWarProject(line 461)

SeamProjectCreator doesn't take this into account and saves wrong values for the folders path.
See SeamProjectCreator#createSeamProjectPreferenes(line 497)

Test Case:
1. New Seam Web Projetc with any name
2. Add jpa facet
3. Select deploy as WAR
4. Finish (if not available do reqired steps)
5. Right click on the project, seam settings
Observe "Model" and "Action / ..." source paths set to <project_name>/src