I have just installed Obarun, and run into an issue with running user services. I followed the wiki for Dbus and DM to get user services to run, however, even though they are enabled they are not initialized.
Here are a few commands which might provide insight into the issue.
Note, I have removed my username from all outputs
doas 66-intree -zg
Name         : boot
Initialized  : yes
Enabled      : no
Starts after : None
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(207,Enabled,classic) tty-earlier@ tty12
               |-(down,Enabled,oneshot) setenv@ <username>
               |-(0,Enabled,longrun) svscan@ <username>-log
               |-(0,Enabled,longrun) svscan@ <username>
               |-(down,Enabled,module) scandir@ <username>
               |-(down,Enabled,oneshot) mount-run@ <username>
               |-(down,Enabled,module) boot-user@ <username>
               |-(down,Enabled,oneshot) system-hostname
               |-(down,Enabled,oneshot) mount-run
               |-(down,Enabled,oneshot) populate-run
               |-(down,Enabled,oneshot) mount-tmp
               |-(down,Enabled,oneshot) populate-tmp
               |-(down,Enabled,oneshot) mount-proc
               |-(down,Enabled,oneshot) mount-sys
               |-(down,Enabled,oneshot) populate-sys
               |-(down,Enabled,oneshot) mount-dev
               |-(down,Enabled,oneshot) mount-pts
               |-(down,Enabled,oneshot) mount-shm
               |-(down,Enabled,oneshot) populate-dev
               |-(down,Enabled,oneshot) mount-cgroups
               |-(down,Enabled,bundle) 00
               |-(down,Enabled,oneshot) system-hwclock
               |-(down,Enabled,oneshot) modules-kernel
               |-(down,Enabled,oneshot) system-random
               |-(down,Enabled,oneshot) modules-system
               |-(down,Enabled,oneshot) system-sysctl
               |-(264,Enabled,longrun) udevd-log
               |-(440,Enabled,longrun) udevd
               |-(down,Enabled,oneshot) udevadm
               |-(down,Enabled,oneshot) system-fontnkey
               |-(down,Enabled,bundle) all-Mount
               |-(down,Enabled,oneshot) system-fsck
               |-(down,Enabled,oneshot) mount-fstab
               |-(down,Enabled,bundle) all-System
               |-(down,Enabled,oneshot) mount-rw
               |-(down,Enabled,oneshot) mount-netfs
               |-(down,Enabled,oneshot) local-loop
               |-(down,Enabled,oneshot) local-sethostname
               |-(down,Enabled,oneshot) local-time
               |-(down,Enabled,oneshot) local-authfiles
               |-(down,Enabled,oneshot) local-tmpfiles
               |-(down,Enabled,oneshot) local-dmesg
               |-(down,Enabled,bundle) all-Local
               |-(down,Enabled,oneshot) all-Runtime
               |-(down,Enabled,bundle) All
               |-(817,Enabled,longrun) tty-rc@ tty2
               |-(818,Enabled,longrun) tty-rc@ tty1
               `-(down,Enabled,module) boot@ system

Name         : default
Initialized  : yes
Enabled      : yes
Starts after : None
Current      : yes
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(707,Enabled,classic) sshd-log
               |-(706,Enabled,classic) sshd
               |-(722,Enabled,longrun) dbus-log
               `-(726,Enabled,longrun) dbus

Name         : network
Initialized  : yes
Enabled      : yes
Starts after : default
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(747,Enabled,longrun) connmand-log
               `-(751,Enabled,longrun) connmand

Name         : user
Initialized  : yes
Enabled      : yes
Starts after : default network
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(up,Enabled,oneshot) setenv@ <username>
               |-(782,Enabled,longrun) svscan@ <username>-log
               |-(809,Enabled,longrun) svscan@ <username>
               |-(up,Enabled,module) scandir@ <username>
               |-(up,Enabled,oneshot) mount-run@ <username>
               `-(up,Enabled,module) boot-user@ <username>

Name         : default
Initialized  : no
Enabled      : yes
Starts after : None
Current      : yes
Allowed      : <username>
Symlinks     : svc->source db->source
Contents     : /
               |-(0,Enabled,longrun) dbus-session@ <username>-log
               `-(0,Enabled,longrun) dbus-session@ <username>
I have noticed that boot-user@ <username> doesn't seem to export $XDG_RUNTIME_DIR, even though it is the only option, which is uncommented within its configuration. 
doas 66-env -t user -e nvim boot-user@ <username>

# # Uncomment it to use a display manager.
# # Can be any display manager as long as the
# # corresponding frontend file exist on your system
# # e.g sddm,lightdm,...
# # It also prepare the .xsession file.

# DISPLAY_MANAGER=sddm

# # Uncomment it to use a console tracker.
# # Can be any console tracker as long as the
# # corresponding frontend file exist on your system
# # e.g consolekit,elogind,...

# CONSOLE_TRACKER=consolekit

# # Create and mount the XDG_RUNTIME directory
# # at /run/user/<username> [yes|no]

XDG_RUNTIME=!yes

# # Command to use in your .xinitrc
# # to launch your desktop e.g.: openbox-session.
# # If commented the .xinitrc file is not configured.

# DESKTOP_CMDLINE=!jwm
and i have run: 
66-enable -t boot -F boot-user@ <username>
as root, so I do believe the changes should have taken effect

If I am missing something obvious, I do apologize, I am not yet fully used to 66 & s6.
You did a little mistake, your command should be 
# 66-enable -t user -F boot-user@ <username>
and not 
# 66-enable -t boot -F boot-user@ <username>
The -t option specify the tree to use to enable the service. So you enabled the boot-user@ at the wrong tree. The result is a conflict between the service enable at the boot tree and the same service enabled at the user tree :).
So, remove the one at the boot tree 
# 66-disable -t boot boot-user@ <username>
then reboot
That is my bad, I did write: 
66-enable -t user -F boot-user@ <username>
I don't know why I wrote that in my post. To be sure, I even my zsh history to be sure, and I can't find 
66-enable -t boot -F boot-user@ <username>
anywhere in it.
I don't know what you did exactly, the fact is that the service boot-user@ <username> have noting to do in the boot tree. So, just disable it and reboot
My bad, I don't know how boot-user@ got into the boot tree, as I haven't enabled it in that tree, but I have now run 
66-disable -t boot boot-user@ <username>
and rebooted however, still no luck with getting my user service tree to initialize 
66-intree -zg

Name         : default
Initialized  : no
Enabled      : yes
Starts after : None
Current      : yes
Allowed      : <username>
Symlinks     : svc->source db->source
Contents     : /
               |-(0,Enabled,longrun) dbus-session@ <username>-log
               `-(0,Enabled,longrun) dbus-session@ <username>
I am not sure what I am missing.
doas 66-intree -cg

Name         : boot
Initialized  : yes
Enabled      : no
Starts after : None
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(213,Enabled,classic) tty-earlier@ tty12
               |-(unitialized,Disabled,oneshot) setenv@ <username>
               |-(0,Disabled,longrun) svscan@ <username>-log
               |-(0,Disabled,longrun) svscan@ <username>
               |-(unitialized,Disabled,module) scandir@ <username>
               |-(unitialized,Disabled,oneshot) mount-run@ <username>
               |-(unitialized,Disabled,module) boot-user@ <username>
               |-(up,Enabled,oneshot) system-hostname
               |-(up,Enabled,oneshot) mount-run
               |-(up,Enabled,oneshot) populate-run
               |-(up,Enabled,oneshot) mount-tmp
               |-(up,Enabled,oneshot) populate-tmp
               |-(up,Enabled,oneshot) mount-proc
               |-(up,Enabled,oneshot) mount-sys
               |-(up,Enabled,oneshot) populate-sys
               |-(up,Enabled,oneshot) mount-dev
               |-(up,Enabled,oneshot) mount-pts
               |-(up,Enabled,oneshot) mount-shm
               |-(up,Enabled,oneshot) populate-dev
               |-(up,Enabled,oneshot) mount-cgroups
               |-(up,Enabled,bundle) 00
               |-(up,Enabled,oneshot) system-hwclock
               |-(up,Enabled,oneshot) modules-kernel
               |-(up,Enabled,oneshot) system-random
               |-(up,Enabled,oneshot) modules-system
               |-(up,Enabled,oneshot) system-sysctl
               |-(259,Enabled,longrun) udevd-log
               |-(432,Enabled,longrun) udevd
               |-(up,Enabled,oneshot) udevadm
               |-(up,Enabled,oneshot) system-fontnkey
               |-(up,Enabled,bundle) all-Mount
               |-(up,Enabled,oneshot) system-fsck
               |-(up,Enabled,oneshot) mount-fstab
               |-(up,Enabled,bundle) all-System
               |-(up,Enabled,oneshot) mount-rw
               |-(up,Enabled,oneshot) mount-netfs
               |-(up,Enabled,oneshot) local-loop
               |-(up,Enabled,oneshot) local-sethostname
               |-(up,Enabled,oneshot) local-time
               |-(up,Enabled,oneshot) local-authfiles
               |-(up,Enabled,oneshot) local-tmpfiles
               |-(up,Enabled,oneshot) local-dmesg
               |-(up,Enabled,bundle) all-Local
               |-(up,Enabled,oneshot) all-Runtime
               |-(up,Enabled,bundle) All
               |-(796,Enabled,longrun) tty-rc@ tty2
               |-(797,Enabled,longrun) tty-rc@ tty1
               `-(up,Enabled,module) boot@ system

Name         : default
Initialized  : yes
Enabled      : yes
Starts after : None
Current      : yes
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(685,Enabled,classic) sshd-log
               |-(686,Enabled,classic) sshd
               |-(701,Enabled,longrun) dbus-log
               `-(705,Enabled,longrun) dbus

Name         : network
Initialized  : yes
Enabled      : yes
Starts after : default
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(726,Enabled,longrun) connmand-log
               `-(730,Enabled,longrun) connmand

Name         : user
Initialized  : yes
Enabled      : yes
Starts after : default network
Current      : no
Allowed      : root
Symlinks     : svc->source db->source
Contents     : /
               |-(up,Enabled,oneshot) setenv@ <username>
               |-(761,Enabled,longrun) svscan@ <username>-log
               |-(788,Enabled,longrun) svscan@ <username>
               |-(up,Enabled,module) scandir@ <username>
               |-(up,Enabled,oneshot) mount-run@ <username>
               `-(up,Enabled,module) boot-user@ <username>
I noticed that boot-user@ is still listed within the boot tree. Might this be the issue?
to remove definitively the boot-user@ service from your boot 
# 66-disable -t boot -F boot-user@ <username>
How do you start your X session?
Since all trees and services appear (must appear after disabling the boot tree user module) are OK, what is the problem now?
The disabled services if they still appear as disabled in 66-intree after a reboot the other option is to run 66-update to make them disappear.

To me the last output looks ok, other than listing the disabled services/module for boot-user inside boot, which is not a functionality problem, it is just the history of the tree.
My apologies, it seems I have misunderstood how 66 user services function. If I am correct, you are supposed to run 
66-all up
as a normal user on each reboot, be it manually, or handeled by something like xinit.
If the tree is enabled % 66-tree -t "user-tree-name" -E

then it will start as soon as you login whether tty or DM, and as long as the boot-user module is enabled by root.

For root any tree that is enabled will be activated after boot completes and if there is a sequence (like start after net tree). Disabled trees need 66-all up/down to be activated deactivated.
Odd, both boot-user@ is enabled by root, and my user tree is enabled, however, upon each login, my user tree is not marked as initialized. 
66-intree -zg

Name         : default
Initialized  : no
Enabled      : yes
Starts after : None
Current      : yes
Allowed      : <username>
Symlinks     : svc->source db->source
Contents     : /
               |-(0,Enabled,longrun) dbus-session@ <username>-log
               `-(0,Enabled,longrun) dbus-session@ <username>
Issuing 
66-all up
as normal initializes the services until next reboot
A distinction need to be made between the boot-user@ which is a root service and service for regular user.
The boot-user@ prepare the necessary to be able to launch service as regular user. So, if the tree containing the boot-user@ is enabled then the scandir for the regular user will be brought up.
Now, this doesn't mean that tree of regular user(and so, service inside it) will be started. You need to start it by e.g the 66-all up command like you said. You have many solution for this, the most used here is to launch this command by your .xinitrc or by your .xsession (dependending if you use a DM or not).

This behavior will change in a near future cause of the new utlogd program...
I was under the impression that when you use 66-env to configure the boot-user@ module the .xsession/.xinitrc that are produced contain the 66-all up command.

Alternatively if you use the default user shell zsh then you can add 66-all up to .zlogin.

I am sorry if I confused you, I rarely just for 66 testing do I use boot-user@
Thank you very much to the both of you. I have now add 
 66-all up
to my .zhhrc file and everything works as expected. Perhaps a note about this behaviour should be added to the wiki?
I think the .zshrc is best for defining your shell environment not to execute commands. The .zlogin is a better place to add it, I think. If you make more trees with other user functions/services you can specify the tree you want up with 66-all.

66-all -t treename1 up
Reckon you're right. How do I mark as solved?
How do I mark as solved?
By editing the very first post of the thread.

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