Here's some examples on how to create a mod that will modify another mod, for example X-Com Files with directly editing the X-Com Files mod files.
Create your own folder in the mods directory, and make sure to add your own `metadata.yml` file, then I'd suggest downloading other peoples mods and reviewing the files, content, organization structure etc. I've done some mods in the past, but over time the format and structure, like what to name the files (optional, but more clarifying what in the files, like picture names or .rul file names can be very helpful.)
.../openxcom/
.../openxcom/mods/
.../openxcom/mods/my_new_mod/
.../openxcom/mods/my_new_mod/metadata.yml
Then in your mod folder create a Ruleset directory where all the .rul files go , etc for Resources (images), Language (text and translations), etc...
I'd recommend starting small on just trying to make a mod that changes a single aspect, property, image, etc and build from there.
Solarius Scorch has done an amazing job on the X-Com Files mod... I'm constantly going to and referencing his mods source files as an example of a change or aspect that I want to implement in my mod work.