Sorting by directory is not my preferance, I don't care for it on the SOTAS site either. But that is a personal thing, I can deal with it.
But adding "The" and sorting "The Dominion" under "T" is just too confusing. You really should change it to "Dominion (B)" or something like that and sort it under "D" after the DS9 Dominion shipset.
Geoschmo