I have used the u' prefix, my user-config contains "usernames['wikipedia']['cs'] = u'HypoBOT'"

My console endcoding is set to 'utf-8' and transliteration_target to console_encoding.

That your username is in unicode doesn't have anything to do with the other warnings. And if you use 'utf-8' it should be str, but maybe unicode_literals is inherited from the config2 module. But if you set transliteration_target to the value of console_encoding it should be the same type. I'll try some tests on my own. Could you maybe show the lines where you define both?

Okay I've checked and “user-config.py” is read with unicode_literals so it doesn't matter if you define anything using 'foo' or u'foo' because both are now unicode. But I couldn't get the transliteration_target warning.
This is a snippet from my “user-config.py”:

password_file = '.passwd'                                                       
print(type(password_file))                                                      
console_encoding = 'utf-8'                                                      
transliteration_target = console_encoding

And it's not importing anything but this is the result:

>>> import pywikibot
<type 'unicode'>
WARNING: Type of 'console_encoding' changed
         Was: <type 'str'>
         Now: <type 'unicode'>

My user-config.py

password_file= 'passfile.txt'

transliteration_target = console_encoding
cosmetic_changes = True
console_encoding = 'utf-8'

AH you set the transliteration_target before console_encoding. Then it makes sense :) console_encoding is by default str and transliteration_target is set to 'not set' which is unicode. Then you set transliteration_target to the value of console_encoding so to a str and then you change console_encoding to 'utf-8' which is also unicode. So the result is as the warning presents:

• transliteration_target changed from unicode ('not set') to str (console_encoding → sys.stdout.encoding)
• console_encoding changed from str (sys.stdout.encoding) to unicode ('utf-8')

Good that is this mystery solved :)

Ok, I changed the transliteration target back to none. But I cant test if the WARNING dissapeared since replace.py doesnt proceed with non-ascii chars (as in T95803)

is there anything left to do here? should config2 automatically upgrade any str from user-config.py to be unicode?

With gerrit 219589 we might be able to do that separately and not just update all strings into unicodes.

In T95810#1391903, @XZise wrote:

With gerrit 219589 we might be able to do that separately and not just update all strings into unicodes.

That has been merged.. ;-)