The first checkbox adds the primary user to the sudo group.
The second checkbox does the above and also disables the root password and edits two files in your home so that admin apps will ask for your user password instead of a root pass.

~/.gconf/apps/gksu/%gconf.xml
~/.su-to-rootrc

I don't have a good answer for your second question, but I have seen similar behavior - apps requiring root privileges either won't start from the menu or if the user is in the sudo group, those apps start without asking for password. Here's one of several discussions about it. To find more, search the forum for terms like policykit, polkit, consolekit, udisks, libpam.
https://dev1galaxy.org/viewtopic.php?id=675

One workaround would be to edit the .desktop files for the affected apps. For example, edit /usr/share/applications/synaptic.desktop and change
Exec=synaptic-pkexec
to
Exec=gksu synaptic
or something like
xterm -e 'su -c synaptic'

This might also work (please let me know if you try it.)
sudo synaptic

If/when gksu goes away, you can edit the Exec line in the .desktop file to use xterm. For example:

Exec=xterm -e 'su -c synaptic'

An xterm will pop up to let you enter the root password.

I can't explain why it would be gtk3 related, but I can offer a way to test that theory. Here's a yad package compiled with support for gtk2 instead of gtk3. Install this one and see if it does the same thing. (sorry, no i386 package)
http://distro.ibiblio.org/refracta/file … _amd64.deb

Sorry to say that palemoon is not in the devuan repo. You're getting a false positive.

Your system:

palemoon is already the newest version (27.7.2~repack-1).

My system:

palemoon is already the newest version.
$ apt-cache policy palemoon
palemoon:
  Installed: 27.3.0~repack-1
  Candidate: 27.3.0~repack-1
  Version table:
 *** 27.3.0~repack-1 0
        100 /var/lib/dpkg/status

Different versions, but in each case it's the newest version that apt can see.

I've thought about adding extlinux support to refractainstaller, but I didn't think there was much interest. Nice to see that there is. I've also thought about adding support for grub to refracta2usb. Maybe those things will actually happen some time.

So, uh, what is /usr/src/refracta-tools and where did that come from?

It's safe and normal to have multiple versions of gcc. If you upgrade from one relase to another, you will accumulate versions of gcc. In fact, I've usually found it necessary to have multiple versions for properly compiling modules - debian typically ships with a version of gcc that's newer than the one that was used to compile the kernel. The proprietary nvidia installer complains if there's a mis-match of gcc versions.

Looks like there's a newer version of 4.9 in jessie-security:

~$ apt-cache policy gcc-4.8
gcc-4.8:
  Installed: 4.8.4-1
  Candidate: 4.8.4-1
  Version table:
 *** 4.8.4-1 0
        500 http://pkgmaster.devuan.org/merged/ jessie/main amd64 Packages
        500 http://auto.mirror.devuan.org/merged/ jessie/main amd64 Packages
        500 http://debian.csail.mit.edu/debian/ jessie/main amd64 Packages
        100 /var/lib/dpkg/status

~$ apt-cache policy gcc-4.9
gcc-4.9:
  Installed: 4.9.2-10
  Candidate: 4.9.2-10+deb8u1
  Version table:
     4.9.2-10+deb8u1 0
        500 http://pkgmaster.devuan.org/merged/ jessie-security/main amd64 Packages
        500 http://auto.mirror.devuan.org/merged/ jessie-security/main amd64 Packages
 *** 4.9.2-10 0
        500 http://pkgmaster.devuan.org/merged/ jessie/main amd64 Packages
        500 http://auto.mirror.devuan.org/merged/ jessie/main amd64 Packages
        500 http://debian.csail.mit.edu/debian/ jessie/main amd64 Packages
        100 /var/lib/dpkg/status

After our previous exchange, I checked my laptop, and the default governer was powersave. Good for a laptop, but that's where I build isos. Been using cpufrequtils since then, and I just now installed and tried linux-cpupower.

cpupower set -b 0 gives me slightly higher speeds than cpufreq-set -g performance but in both cases, speeds drop at idle. I don't know if recompiling the kernel without the governers is necessary or even possible or if it would work. You might be able to just unload the module(s) to get constant full speed.

You could have at least provided the bug number in your post. I assume you mean this one:
https://bugs.devuan.org/db/12/129.html

I suggest you do the installation in your first chosen language, and then install lxdm afterward to be able to switch languages at the login screen.

Good observation. Most of the repository is empty. You will only find packages that were changed by devuan in the devuan repositories. The packages will be in /pool, but you must be sure to get the right version.The way amprolla works is to merge the debian repos with the devuan repos and serve you the correct packages for your system.

If you want to download any packages in devuan:

apt-get download <package>
or
aptitude download <package>

If you want to download from the web, use a devuan repo url for packages that have been modified by devuan and go to packages.debian.org for packages we have not modified. DO NOT ERR! (It's safer to use the package manager to get the packages.)

I believe someone is working on a web interface for searching files, but I don't know the current status.

I think the libpolkit packages you get depend on which desktop and login manager you install. In some cases, libpolkit-backend-1-0-consolekit is needed instead of the elogind backend. There may be more changes planned for that mess.

The libsystemd0 dependency issue is well known. It would be nice to get rid of it, but it's in more and more packages with each release. And it does nothing if systemd isn't present and running. And systemd is not present and cannot be installed from devuan repositories.

I installed lxde yesterday and was getting the same error (No session for pid#). The pid is always for lxpolkit. Removing lxpolkit solved it for me. Shutdown buttons were working before and after removing lxpolkit.

I also experimented with running 'pam-auth-update' to alternately disable elogind or consolekit, and it seems to be working normally with either one.

Here's a list of the kits that were installed.

user@devuan:~$ dpkg -l | grep consolekit
ii  consolekit                             0.4.6-6                           amd64        framework for defining and tracking users, sessions and seats
ii  libpolkit-backend-1-0-consolekit:amd64 0.105-18+devuan2.4                amd64        PolicyKit backend API
user@devuan:~$ dpkg -l | grep policykit
ii  lxqt-policykit                         0.11.1-1                          amd64        LXQt authentication agent for PolicyKit
ii  lxqt-policykit-l10n                    0.11.2-1                          all          Language package for lxqt-policykit
ii  policykit-1                            0.105-18+devuan2.4                amd64        framework for managing administrative policies and privileges
ii  policykit-1-gnome                      0.105-6                           amd64        authentication agent for PolicyKit
user@devuan:~$ dpkg -l | grep elogind
ii  elogind                                234.4-1+devuan1.5                 amd64        user, seat and session management daemon
ii  libelogind0:amd64                      234.4-1+devuan1.5                 amd64        user, seat and session management library
ii  libpam-elogind:amd64                   234.4-1+devuan1.5                 amd64        elogind PAM module
user@devuan:~$ dpkg -l |grep polkit
ii  libpolkit-agent-1-0:amd64              0.105-18+devuan2.4                amd64        PolicyKit Authentication Agent API
ii  libpolkit-backend-1-0-consolekit:amd64 0.105-18+devuan2.4                amd64        PolicyKit backend API
ii  libpolkit-gobject-1-0-systemd:amd64    0.105-18+devuan2.4                amd64        PolicyKit Authorization API
ii  libpolkit-qt5-1-1:amd64                0.112.0-5                         amd64        PolicyKit-qt5-1 library
rc  lxpolkit                               0.5.3-2                           amd64        LXDE PolicyKit authentication agent

(Edited to add 'dpkg -l |grep polkit')

Edit2: I added
libpolkit-backend-1-0-elogind (0.105-18+devuan2.4)
libpolkit-gobject-1-0-elogind (0.105-18+devuan2.4)

That removed libpolkit-backend-1-0-consolekit and libpolkit-gobject-1-0-systemd. I had to run 'pam-auth-update' and enable elogind to get shutdown buttons working again.