Rudder

it tries to remove '/usr/share/ncf/tree' and '/usr/share/ncf/tools'
then we have

Preparing to unpack .../rudder-webapp_6.1.0~rc3~git202006050100-debian9_amd64.deb ...
/etc/init.d/rudder-slapd: 282: .: Can't open /opt/rudder/etc/rudder-slapd.conf
/etc/init.d/rudder-jetty: line 289: cd: /opt/rudder/jetty/: No such file or directory

also, webapp logs show that rudder-slapd is stoped before rudder-webapp, so webapp is partially broken during upgrade, but it should be stopped

Unpacking rudder-agent (6.1.0~rc3~git202006050100-debian9) over (5.0.18~rc1~git202006050209-debian9) ...
(Reading database ... 47283 files and directories currently installed.)
Removing rudder-inventory-endpoint (5.0.18~rc1~git202006050209-debian9) ...
Removing rudder-inventory-ldap (5.0.18~rc1~git202006050209-debian9) ...
INFO: Stopping rudder-slapd... Done
dpkg: ncf: dependency problems, but removing anyway as you requested:
 ncf-api-virtualenv depends on ncf.
 rudder-techniques depends on ncf (>> 5.0.18~rc1~git000000000000).
 rudder-techniques depends on ncf (<< 5.0.18~rc1~git999999999999).
 rudder-techniques depends on ncf (>> 5.0.18~rc1~git000000000000).
 rudder-techniques depends on ncf (<< 5.0.18~rc1~git999999999999).

Removing ncf (5.0.18~rc1~git202006050209-debian9) ...
dpkg: warning: while removing ncf, directory '/usr/share/ncf/tree' not empty so not removed
dpkg: warning: while removing ncf, directory '/usr/share/ncf/tools' not empty so not removed
dpkg: ncf-api-virtualenv: dependency problems, but removing anyway as you requested:
 rudder-webapp depends on ncf-api-virtualenv (>> 5.0.18~rc1~git000000000000).
 rudder-webapp depends on ncf-api-virtualenv (<< 5.0.18~rc1~git999999999999).
 rudder-webapp depends on ncf-api-virtualenv (>> 5.0.18~rc1~git000000000000).
 rudder-webapp depends on ncf-api-virtualenv (<< 5.0.18~rc1~git999999999999).

Removing ncf-api-virtualenv (5.0.18~rc1~git202006050209-debian9) ...
dpkg: rudder-jetty: dependency problems, but removing anyway as you requested:
 rudder-webapp depends on rudder-jetty (>> 5.0.18~rc1~git000000000000).
 rudder-webapp depends on rudder-jetty (<< 5.0.18~rc1~git999999999999).
 rudder-webapp depends on rudder-jetty (>> 5.0.18~rc1~git000000000000).
 rudder-webapp depends on rudder-jetty (<< 5.0.18~rc1~git999999999999).

Removing rudder-jetty (5.0.18~rc1~git202006050209-debian9) ...
dpkg: rudder-techniques: dependency problems, but removing anyway as you requested:
 rudder-webapp depends on rudder-techniques (>> 5.0.18~rc1~git000000000000); however:
  Package rudder-techniques is to be removed.
 rudder-webapp depends on rudder-techniques (<< 5.0.18~rc1~git999999999999); however:
  Package rudder-techniques is to be removed.
 rudder-webapp depends on rudder-techniques (>> 5.0.18~rc1~git000000000000); however:
  Package rudder-techniques is to be removed.
 rudder-webapp depends on rudder-techniques (<< 5.0.18~rc1~git999999999999); however:
  Package rudder-techniques is to be removed.

Removing rudder-techniques (5.0.18~rc1~git202006050209-debian9) ...
(Reading database ... 43684 files and directories currently installed.)
Preparing to unpack .../rudder-server-relay_6.1.0~rc3~git202006050100-debian9_amd64.deb ...
Unpacking rudder-server-relay (6.1.0~rc3~git202006050100-debian9) over (5.0.18~rc1~git202006050209-debian9) ...
Setting up python3-six (1.10.0-3) ...
Setting up python3-urllib3 (1.19.1-1) ...
Setting up python3-pkg-resources (33.1.1-1) ...
Setting up python3-chardet (2.3.0-2) ...
Setting up python3-requests (2.12.4-1) ...
Setting up python3-lxml (3.7.1-1) ...
Setting up libonig4:amd64 (6.1.3-2) ...
Setting up libjq1:amd64 (1.5+dfsg-1.3) ...
Setting up jq (1.5+dfsg-1.3) ...
Setting up rudder-agent (6.1.0~rc3~git202006050100-debian9) ...
Installing new version of config file /etc/bash_completion.d/rudder.sh ...
Installing new version of config file /etc/profile.d/rudder-agent.sh ...
INFO: Scheduling an inventory during next run...
INFO: Agent certificate is missing, creating it... Done
INFO: No disable file detected and no agent executor process either. Restarting agent service... Done
FINISH: Rudder agent check ran properly, please look at messages above to see if there has been any error.
Setting up rudder-server-relay (6.1.0~rc3~git202006050100-debian9) ...
Installing new version of config file /etc/apache2/sites-available/rudder.conf ...
Installing new version of config file /opt/rudder/etc/rudder-apache-relay-common.conf ...
Installing new version of config file /opt/rudder/etc/rudder-apache-relay-ssl.conf ...
Installing new version of config file /etc/cron.d/rudder-relay ...
Installing new version of config file /etc/sudoers.d/rudder-relay ...
INFO: Creating users ... Done
INFO: Configuring systemd services... Done
INFO: Starting services... Done
INFO: rudder-server-relay setup complete.
(Reading database ... 41744 files and directories currently installed.)
Preparing to unpack .../rudder-webapp_6.1.0~rc3~git202006050100-debian9_amd64.deb ...
/etc/init.d/rudder-slapd: 282: .: Can't open /opt/rudder/etc/rudder-slapd.conf
/etc/init.d/rudder-jetty: line 289: cd: /opt/rudder/jetty/: No such file or directory
********************************************************************************
INFO: dpkg may ask you if you want to replace rudder-web.properties or          
INFO: inventory-web.properties with the maintainer version if you modified it.  
INFO:                                                                           
INFO: If you accept, please keep in mind that you will lose any manual          
INFO: modification in this file, like the syslog port or the workflows and will 
INFO: certainly have to add them again.                                         
INFO:                                                                           
INFO: We recommend that you respond NO to this question                         
INFO: ('keep your currently-installed version'). Rudder's upgrade script will   
INFO: take care of this automatically.                                          
INFO:                                                                           
********************************************************************************
Unpacking rudder-webapp (6.1.0~rc3~git202006050100-debian9) over (5.0.18~rc1~git202006050209-debian9) ...
dpkg: warning: unable to delete old directory '/var/rudder/inventories/historical': Directory not empty
dpkg: warning: unable to delete old directory '/var/rudder/configuration-repository/ncf': Directory not empty
dpkg: warning: unable to delete old directory '/var/log/rudder/reports': Directory not empty
Selecting previously unselected package python3-bs4.
Preparing to unpack .../python3-bs4_4.5.3-1_all.deb ...
Unpacking python3-bs4 (4.5.3-1) ...
Selecting previously unselected package python3-webencodings.
Preparing to unpack .../python3-webencodings_0.5-2_all.deb ...
Unpacking python3-webencodings (0.5-2) ...
Selecting previously unselected package python3-html5lib.
Preparing to unpack .../python3-html5lib_0.999999999-1_all.deb ...
Unpacking python3-html5lib (0.999999999-1) ...
Setting up python3-webencodings (0.5-2) ...
Setting up python3-bs4 (4.5.3-1) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Setting up python3-html5lib (0.999999999-1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Setting up rudder-reports (6.1.0~rc3~git202006050100-debian9) ...
INFO: Setting PostgreSQL as a boot service...Synchronizing state of postgresql.service with SysV service script with /lib/systemd/syste
md-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable postgresql
 Done
INFO: Waiting for PostgreSQL to be up... Done
Setting up rudder-webapp (6.1.0~rc3~git202006050100-debian9) ...
Installing new version of config file /opt/rudder/etc/rudder-jetty.conf ...

Configuration file '/opt/rudder/etc/rudder-web.properties'
 ==> Modified (by you or by a script) since installation.
 ==> Package distributor has shipped an updated version.
   What would you like to do about it ?  Your options are:
    Y or I  : install the package maintainer's version
    N or O  : keep your currently-installed version
      D     : show the differences between the versions
      Z     : start a shell to examine the situation
 The default action is to keep your current version.
*** rudder-web.properties (Y/I/N/O/D/Z) [default=N] ? 
Installing new version of config file /opt/rudder/etc/rudder-users.xml ...
Installing new version of config file /opt/rudder/etc/logback.xml ...
Installing new version of config file /opt/rudder/etc/rudder-apache-webapp-ssl.conf ...

Configuration file '/opt/rudder/etc/openldap/slapd.conf'
 ==> Modified (by you or by a script) since installation.
 ==> Package distributor has shipped an updated version.
   What would you like to do about it ?  Your options are:
    Y or I  : install the package maintainer's version
    N or O  : keep your currently-installed version
      D     : show the differences between the versions
      Z     : start a shell to examine the situation
 The default action is to keep your current version.
*** slapd.conf (Y/I/N/O/D/Z) [default=N] ? 
Conf ncf-api-virtualenv disabled.
To activate the new configuration, you need to run:
  systemctl reload apache2
INFO: Creating groups ... Done
INFO: Creating users ... Done
INFO: Removing ncf-api-venv user and group ...userdel: ncf-api-venv mail spool (/var/mail/ncf-api-venv) not found
 Done
INFO: Setting up systemd ...Synchronizing state of rudder-jetty.service with SysV service script with /lib/systemd/systemd-sysv-install
.
Executing: /lib/systemd/systemd-sysv-install enable rudder-jetty
Created symlink /etc/systemd/system/multi-user.target.wants/rudder-jetty.service → /usr/lib/systemd/system/rudder-jetty.service.
Created symlink /etc/systemd/system/rudder-server.service.requires/rudder-jetty.service → /usr/lib/systemd/system/rudder-jetty.service.
Synchronizing state of rudder-slapd.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable rudder-slapd
Created symlink /etc/systemd/system/multi-user.target.wants/rudder-slapd.service → /usr/lib/systemd/system/rudder-slapd.service.
Created symlink /etc/systemd/system/rudder-server.service.requires/rudder-slapd.service → /usr/lib/systemd/system/rudder-slapd.service.
INFO: Restarting rudder-slapd... Done
INFO: Launching script to check if a migration is needed ...
Done
********************************************************************************
Due to incompatibility reasons for this specific version all plugins have been
disabled. Make sure to update your repo index and install the latest version of
your plugins before re-enabling them.

You can use the following commands to upgrade your plugins:
rudder package update
rudder package upgrade-all
********************************************************************************
INFO: Re-generate rudder-lang libraries ...
Done
INFO: Make sure Rudder webapp is started... Done
INFO: Make sure Apache HTTPd is started... Done
Processing triggers for rsyslog (8.24.0-1) ...
Setting up rudder-server-root (6.1.0~rc3~git202006050100-debian9) ...
Synchronizing state of rudder-server.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable rudder-server
Created symlink /etc/systemd/system/multi-user.target.wants/rudder-server.service → /usr/lib/systemd/system/rudder-server.service.
Processing triggers for libc-bin (2.24-11+deb9u1) ...