Full Linux guide
This guide assumes you already have Steam and Jalopy installed, and JaPatcher >=5.1.2 downloaded, and extracted.
First, we need to find Jalopy's game files location, by opening Steam, right clicking on Jalopy, then on Manage, then on Browse local files
This will open a file browser, just copy the location from the navigation bar, and store it somewhere temporarily (e.g. clipboard)
We also need to tell wine to use the native winhttp.dll, found in the game folder.
To do this, right click on Jalopy (in Steam), then on Properties, in General, and write WINEDLLOVERRIDES="winhttp=n,b" %command%
Next, run JaPatcher.exe, either via Wine, either add it as a Non-Steam game in your Steam library, and run it.
A small message should appear, press OK, after which a small window with a large text box should appear.
Paste the path to Jalopy there, as instructed, then press OK.
Now press "Install", and select your desired mod location.
Done!