Not much to show for the log - the forge_upgrade_log is empty (even though I have executed it):

mysql> select * from forge_upgrade_log;
Empty set (0.00 sec)

I'll take a look at this setup.sh script - I'm a bit afraid of loosing data due to reinstallation.
What I did yesterday is that I took a look at all scripts in /usr/share/tuleap/src/db/mysql/updates/2015/ and manually checked that I'm fine with the changes that are required. I don't remember now details but it looks like (modulo my memory):
- I was aligned with all changes up to 201504091644_add_authenticated_user_group.php,
- I can't really say if 201504171343_restore_FRS_owner_group.php was executed or not, the permissions seems right in file system but I can't say if that was due to script actions or them being right from the start
- starting with 201505051630_add_new_password_field.php I had to:
- manually apply changes from 201505051630_add_new_password_field.php
- do nothing with 201505131103_project_admin_can_choose_visibility.php
- do nothing with 201505302300_remove_twitter_widgets.php
- manually apply changes from 201506011450_increase_unix_password_field_size.php
- manually apply changes from 201506031610_add_svn_immutable_tags_whitelist_table.php
- manually apply changes from 201506031658_enlarge_your_tinyint.php
- manually apply changes from 201507152200_increase_session_ip_field_size.php

Feel free to ask for more info/data - I'm eager to find a problem since I'm afraid any future upgrade of my installation is a potential problem.
If you don't need any input from my side you can close the issue.

Best regards
Andrzej

PS. I would advice to improve rpm installation script, that is stop/start services automatically from it and move this manual forgeupgrade script step to rpm post installation part (and probably noting in documentation that from version XXX this step is done automatically during package upgrade) - this would avoid problems with people like me that are spoiled by the linux packaging systems and just assumed that all one need to do is just to upgrade package and it will take care of everything.

Addendum.

I've just found file /usr/share/tuleap/src/db/mysql/database_structure.sql.
Inside I see that password field is part of DB schema for 'user' table so I gather that instead of preventing it's insertion it is now expected to be there. I also has found /usr/share/tuleap/src/db/mysql/updates/2015/201505051630_add_new_password_field.php and inside SQL query to add it to 'user' table. I've run the query and I'm able now to create user.

So I'll close the issue but I'd like to ask first what process was responsible for execution of this php that was supposed to upgrade DB.
Was it this forgeupgrade? How can I double check if all parts of my installation are in sync?

Best regards
Andrzej

Thank you Thomas for devoting some time to this.
Unfortunately I'm still having the same problem.
It is true that I have not run forgeupgrade previously but now it says that:

/usr/lib/forgeupgrade/bin/forgeupgrade --config=/etc/codendi/forgeupgrade/config.ini update
INFO - System up-to-date

Your second link for deployment (especially section for 8.3 "Password storage") made me feel like I'm home ... but having followed the instructions, that is with (and also running script for openfire - I don't have proftpd plugin installed):

# grep hashed /etc/tuleap/conf/local.inc
$sys_keep_md5_hashed_password = 0;

I'm still having the same issue. So the steps I made are:
1. Stopped tuleap&httpd services
2. Run forgeupgrade
3. Added $sys_keep_md5_hashed_password = 0; to local.inc
4. Run redeploy_auth script for IM plugin
5. Started tuleap&httpd

It looks to me like if the point 3 has not yet managed to take an effect since the "INSERT INTO user ..." command still has 'password' column (which is not in the DB table) - perhaps I do not understand how this should be working. I'd like to use the new scheme so my understanding is that the $sys variable should be set to 0 so that hash for password that was previously kept in 'password' column is no longer put in DB.

I'm afraid I still need some help :( - how do I stop DataObjectClass from inserting hashed password to DB? How can I debug this further?

Best regards
Andrzej