Around Pillar release 1.0 (ConfigurationOfPillar 154) the variable embedded was been removed from PRReference in the Pillar project, thus links were no longer listed as embedded. This has the impact of causing Pier's web server to have the root appear without embedded links:

3.1.2-baseline, which has:spec
project: 'Pillar Core' with: [
spec
className: #ConfigurationOfPillar;
versionString: '1.1.2';
loads: #('Pillar-Model' );and this still includes the embedded variables in PRReference (and the methods isEmbedded and the accessors), however this kept Pier from working with Seaside 3.2.
Changing PRReference>>embedded to be the 'embedded' property prevents the need for this variable. The property is a dictionary of values defined in PRObject. In case conversion code is need, run this before importing the new Pier-Model:
PRReference allSubclassesDo: [ :class | class allInstancesDo: [:e | e isEmbedded ifTrue: [ e propertyAt: 'embedded' put: true ] ] ].