All new textures I am adding to the new PK3 file have a defined naming system. Seems that names are limited to 8 characters, so I came up with a system where 4 letters describe the type of texture, two digits give it a serial number, one letter designates a subvariation of the texture and one character is saved for special cases. Except for the 8th character, all other characters are obligatory. Examples: CITY02A is the 2nd city texture's first (basic) variation. CHUR03D is the 3rd church texture's 4th variation. For an example how this works: CITY13A is the basic wall texture using the big green stones. CITY13B is the same texture with a window on it. CITY13C is the same texture with a door on it. These correspond to the old ATOWN13, ATOWNW12 and ATOWND10 (or similar numbers, don't remember exactly) textures, but now they are clearly delineated as variations of the same texture and are shown together in DB2's texture browser.

To be able to use the same nomenclature for flats, I thought maybe wall textures could be 01-70 and floors starting at 71 (up to 99), e.g. CITY13A would be a wall texture, CITY73A would be a floor.

Yep, I agree with that <!-- s:) --><img src="{SMILIES_PATH}/orc2.gif" alt=":)" title="Smile" /><!-- s:) -->.

On further tests, it might make more sense to add a T or an F at the beginning of the name, currently all textures/flats are offered by DB2 when you choose either, so finding a floor texture is pretty difficult. The new version would be to name them e.g. TCITY13A, FCITY12B etc. Not sure whether this would make sense though - it offers the benefit of seeing at a glance whether a texture is meant for flats or walls, OTOH it'd only work really well if all original Hexen textures were re-imported and renamed, meaning all existing maps would have to be changed for the new texture names (of course if a converter could take care of that automatically, this latter would actually be doable).

I guess the question is, do we have some command line tool that can do this conversion automatically using e.g. a conversion table from a text file? I think something similar was done when Heretic maps were converted for KA.

The tool for converting the Heretic maps did something entirely different, it was for converting the maps to support Hexen extended map format, it didn't modified any other data on the WAD files. I don't know if there's any tools for changing texture names on linedefs/sectors... but I'll try to investigate it.