Here is the complete output: https://pastebin.com/p4bsUJj1

update.sh just runs 'apt update && apt dist-upgrade' and then runs git pull on all git repos in a directory.

Trying to 'fix' things:

root@kali:~# apt --fix-broken install
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following additional packages will be installed:
pdfbook
The following NEW packages will be installed:
pdfbook
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
471 not fully installed or removed.
Need to get 0 B/6,982 B of archives.
After this operation, 26.6 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 659516 files and directories currently installed.)
Preparing to unpack .../pdfbook_0.1.0-1kali1_all.deb ...
Unpacking pdfbook (0.1.0-1kali1) ...
dpkg: error processing archive /var/cache/apt/archives/pdfbook_0.1.0-1kali1_all.deb (--unpack):
trying to overwrite '/usr/bin/pdfbook', which is also in package texlive-extra-utils 2018.20190227-2
Errors were encountered while processing:
/var/cache/apt/archives/pdfbook_0.1.0-1kali1_all.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)