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In case it helps anyone:

The .chr file provided in this repository gives the error Incorrect charset file format: /root/hex_lower.chr. I downloaded Github's "raw" url using curl $url -o hex_lower.chr (and checked that it was not the redirect page which I downloaded, it really was a file starting with CHR2 and then binary contents).

I still haven't figured out how to simply specify a charset, either directly or to create a chr file. I guess that would be too convenient. The workaround that I found, to create my own .chr file, is by creating a fake pot file and using --make-charset. Steps to make this work:

1. This is the only contents of ~/.john/john.pot: x:abcdef0123456789

2. Generate the char file: john --make-charset=hex.chr

3. Add it to your john config, in my case /etc/john/john.conf:

    [Incremental:myhex]
    File = /path/to/hex.chr
    MinLen = 8
    MaxLen = 8
    CharCount = 16
   

4. Finally, launch it using: john -i=myhex /etc/shadow (where /etc/shadow is the file you want to crack).