I think the error is not really coming from the Shared Files feature. The Shared Files feature is triggering the index builders as it should when a file changes or is added. But this process invokes all the index builders for all the features. I suspect editing other features such as html content feature would also result in an error since it would also trigger indexing.
I suspect you have a custom or 3rd party feature that was broken by the upgrade because the index builder framework was moved from the mojoPortal.Business.WebHelpers.dll assembly into mojoPortal.Web.dll. But some custom or third party feature still expects it in the old place. All the built in features have been updated, so the built in features cannot cause this error.
The possible solutions:
- re-compile the custom feature so it correctly references the new location of the index builder framework
- remove the index builder configuration file for the custom or 3rd party feature to unplug it so it is not invoked during indexing. The config files that plugin index builders are located under /Setup.ProviderConfig/indexbuilders. Removing the one for the bad custom or 3rd party feature from that folder and then touching web.config to clear the cache should prevent the error from happening but the custom feature will no longer be searchable.
Hope that helps,