Whenever I edit a material, on an already existing model, it gets exported with a new name / path. But the old material remains in automat. With time (and several edits), I end up with unused files (mats) in automat folder.
Question is, is there a way to track all these "leftovers" and remove them?
What are you talking about is simple action of cleaning "rsrc" folder before doing final "build/convert".
Old conversion helper has "Clean 'rsrc'" option and new one by current design has two options for that:
1. "CLEAN RSRC" operator, which directly removes everything that is currently in conversion tools 'rsrc' folder -> cleans it
2. "Auto Clean" option, which will simply again remove everything from 'rsrc' before exporting/converting/packing
Secondly, if I use non-packed mods (in folder state), can we have a checkbox to skip the archiving process, and just copy to a folder, instead?
Well this one is tricky, so easy answer is no as you can simply use "No Compression" and also it's not "just skip archiving"
as I am not copying any converted sources anywhere, instead I am creating zip file directly.
Secondly what you are implying is editing data after conversion, which was never a good/safe solution. If you need to edit sth then edit it in your source mod data. As you will have this "magic" button now, I really don't see why you would have to have everything in "mod" folder...
Would it be possible for the conversion tools to look only at the folders used by the game? Example if I have folder named "Test" in my mod folder, it would not touch it, not copy or convert.
And who is saying that someone else won't use Test directory for doing a mod out of it? There is no restriction on directories in our game (of course game searches for def files and some resources on particular "hardcoded" places, but it doesn't restrict user to use only directories you get from extracted base.scs)
On the other hand you can do that for yourself, open "<conversion_tools/bin/win_x86/tools/resconvert.sii" and see how rules are created, you can simply exclude directories you want by creating your own rules
And there is other more suitable way for you, by creating proper hierarchy:
1. You need dir structure like this:
|- base -> put anything you don't want to be converted in here, make sure this folder is really named "base" as it serves as sibling SCS game hierarchy
|- my_mod_base -> folder where you put your exported models, sii files... that you need in your mod
2. when using BT, set SCS Project Base Path to -> MyModFolder/my_mod_base
3. now you can load textures in BT from "base" and they will be treated the same as they would be inside "my_mod_base"
4. when you will use conversion "MyModFolder/base" will be ignored as you current SCS Project Base Path points to "MyModFolder/my_mod_base"
5. you just got what you wanted in the first place, ignoring any resources you don't want. So in your case "Test" folder would have to be in "base" not in "my_mod_base".
This behaviour is very usefull if you are using any resources from base.scs and you don't want to export or include them in your mod, hance look at the structure on my MapEdit github -> https://github.com/50k-Customs/ETS2-MapEdit