Some ideas about layout.

<COMPANY>/
    <COMPONENT>/ - fixed layout with all optional folders (extept src/)
        doc/
        src/
        shared/ - external libraries used by this component
        examples/

For release planning it would be also good to introduce branches/tags there
to release each of the components separately:

trunk/MyOpenSource/
    HEC/
       RAS/ <---------- current development version of RAS
          src/
          examples/
          ...
    USGS/
       MODFLOW/
          ...
    CUASHI/
       WaterOneFlow/
          ...
       
tags/MyOpenSource/
    HEC/
       RAS-1.0/ <------ SVN copy of the trunk released on DD.MM.YYYY
          src/
          examples/
          ...
       RAS-2.0/  
          src/
          examples/
          ...
    USGS/
       MODFLOW-2005.1/
          ...
       MODFLOW-2008/
          ...