The end-users are players, and for them file names etc. are completely irrelevant.
However, for future additions, modifying the game, and making maps it helps if file names are reflective of what they are. This is already the case for e.g. pyramids:
gaia/ruins/pyramid_great.xml
gaia/ruins/pyramid_minor.xml
structures/kush_pyramid_large.xml
structures/kush_pyramid_small.xml
The folder paths make it clear the former two have a different function than the latter two. Likewise, it would make sense to have fruit and wood trees in separate gaia subfolders, to make it less likely map makers mistakingly pick one functionally different from what they intend. And if at some point there are e.g. different geese, then
birds/goose.xml
gaia/fauna/goose.xml
would make it clear which one flies around and does nothing, and which one can be killed to supply food like other fauna.