I've been working on database-backed websites for the last five years. I've been thinking about the problems of conventional wisdom in this area for at least the last three of those years. And I've been obsessing about hypertext, things not being tree-shaped, and module boundaries for several months.
But only today, I actually had what is possibly the only really profound and interesting thought I've ever had about designing such systems. And of course it's so blindingly obvious, given the context, that I must be incredibly stupid not to have noticed it before :
Decomposition by language is probably a ModularityMistake.