Any application that relies on a set of tables in a database, whether it is a framework or a dedicated application system, still has relationships that must be satisfied to function properly, and I don't think that Liferay is any different.
Extending or overriding the message board functionality, for example, would (should) never lead to violating certain parent/child relationships, i.e. the MBMessageFlag table has a permanent relationship to MBMessage. Sure there may be a need to add functionality or replace functionality, but the relationship would still need to be maintained...
I don't advocate accessing the Liferay database directly, and I'm not sure why the OP was looking at the tables in toad to begin with.
I admit that I have looked at the tables in order to fix errors (data errors, probably as a result of code errors). In the last instance, our 5.2.3 installation was set up to import from AD; through a comedy of errors, an upgrade of MS Exchange resulted in duplicated email addresses in AD, and Liferay started showing exceptions every time the auto-sync to AD fired. Removing the duplicates from AD fixed most of the problems except one - an existing orphaned Group_ record w/ a friendlyURL that prevented the sync from completing properly (an existing orphan Group_ record had a friendlyURL that matched what was being generated by the user creation process during import). Sure, there may have been someplace in Liferay that I might have been able to find the group to delete it, but I did a quick delete statement in the database and all was well.
Had there been FKs set up to begin with, I'm pretty sure that the LDAP/AD sync process would never have failed in the first place (the removal of the user from AD would have had the sync process delete the User_ record which would have correctly cascaded to the Group_ table all on it's own, leaving no orphans).
The point to all of this is that any application can break when the fundamental relationships that it expects to be honored are violated. FKs help to prevent those violations from happening, even for portal frameworks.
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