Currently DelftShell uses .NET application configuration options defined in DelftShell.Loader.exe.config. Actually these options are copied from app.config in the project sources, VS does it automatically during compilation.

Additionally there is a way to define user-specific settings, see for example DelftShell/Properties/Settings.settings file.

When DelftShell is started from the VS - it loads all plugins from the following folder:

apps\DelftShell\modules\DelftShell.Loader\bin\
   plugins\
      Habitat\
         DelfShell.Plugins.Habitat.dll
      Verkenner\
         DelfShell.Plugins.Verkenner.dll
      Sobek\
         DelfShell.Plugins.Sobek.dll
      ...
   Debug\
      DelftShell.Loader.exe
      DelftShell.Loader.exe.config ....... application settings file (XML)
      DelftShell.dll
      DelftTools.Core.dll
      DelftTools.Gui.dll
      ...
   Release\
      ...

User settings file is generated automatically at each exit of DelftShell:

C:\Documents and Settings\donchyt\Local Settings\Application Data\Delft_Hydraulics\DelftShell.Loader.exe...\1.0.0.0\user.config

If you want to load only specific plugin - put the following option there:

<setting name="loadedPluginsFilterExpression" serializeAs="String">
     <value>Habitat</value>
</setting>

It can contain plugin name or any other .NET Regular Expression.