Pywikibot creates pywikibot.lwp with 644 mode by default. Checks that were implemented eariler automatically changes the mode on next run of any script which triggers the run (I believe login is the only one action).
This should be changed, so the checks will trigger only if user manually changes the mode (then a warning will be more than appropriate).
See this, which was executed right after I freshly clonned PWB and generated user files.
testovaci@notebook:~$ python ~/pywikibot/pwb.py login -family:species -lang:species WARNING: /home/testovaci/pywikibot/pywikibot/tools/__init__.py:2015: UserWarning: File /home/testovaci/pywikibot/user-password.py had 600 mode; converted to 700 mode. warn(warn_str.format(filename, st_mode - stat.S_IFREG, mode)) Logging in to species:species as UrbanecmBot@BotTest WARNING: /home/testovaci/pywikibot/pywikibot/tools/__init__.py:2015: UserWarning: File /home/testovaci/pywikibot/pywikibot.lwp had 664 mode; converted to 600 mode. warn(warn_str.format(filename, st_mode - stat.S_IFREG, mode)) Logged in on species:species as UrbanecmBot.