We use exactly the same method, which you mentioned, to store Seam 
project settings in .setting folder.
See 
org.jboss.tools.seam.ui.preferences.SeamSettingsPreferencePage.storeSettings()

Rob Stryker wrote:
  

Hi All:

I previously thought using an project-scoped preference eclipse 
preference node would properly store the data in your project so that 
the preference is a per-project setting and so that also these 
preferences can be shared.

This is not the case, as from this article:

    * /Project scope/. This scope stores values that are specific to a
      single project in your workspace, such as code formatter and
      compiler settings. Note that this scope is provided by the
      org.eclipse.core.resources plug-in, which is not included in the
      Eclipse Rich Client Platform. This scope will not exist in
      applications that don’t explicitly include the resources plug-in.

Settings saved in the following method, while on a project-scope, are 
still saved in the workspace, which means they're not persisted to cvs / 
svn / etc.

IScopeContext context = new ProjectScope(project);
IEclipsePreferences node = context.getNode(qualifier);
if (node != null)
node.putDouble(IJBossESBFacetDataModelProperties.ESB_PROJECT_VERSION, 2.0);


Does anyone know how to actually put some settings inside the .settings 
folder of a project the way JDT and WTP do? Thanks.

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