In Quake2 for textures store uses .WAL files (one texture per one file), not .WAD. 

Ok so is there any tool for that? 

Try launch Wally under wine. But Wally haven't batch convert images to Q2 .wal, you must be convert all your images manually.

https://www.quaddicted.com/files/mirrors/ftp.telefragged.com/wally/ 

Wally is not cli tool, it is gui tool. 

It doesn't seem to require many dependencies for it to run fine. I've been using Wally in Linux thru wine for years. Batch converter never worked for a damn, but exporting to WAL works fine. 

I was tired when I wrote #5, so forgive me if it went astray. ;-p

I haven't used wally in wine-staging 2.0rc3 for Quake2 stuff lately and must of been thinking about another program because YES the batch converter works fine. I just converted a couple hundred Q2 Weapons Factory wal files back and forth between image formats and the process was quick and the files were fine.

Most older programs work fine in WINE. Wally and Photoshop 7 being of those along with the Quake2 WAL plugin for it. For the WTF issues running the occassional windows apps I have a old stripped down version of windows XP and freely available and legal virtual image of Windows 7. 

If I haven't been clear: I really need a CLI tool. I have way too many texture files to use something like Wally manually.

If it runs in wine that's ok too, but I don't have much use for a GUI tool. 

pcx2wal ...

https://www.quaddicted.com/files/idgames2/quake2/utils/graphics_edit/texture_utils/

You'd have to convert the images to .pcx first, but there are countless ways to do that.