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I recently answered a question on StackOverflow about this, and have now experienced it twice myself - once with ST2 on OSX, and just now with ST3 on WinXP. Interestingly, it did not occur with ST2 on XP.
What happens is that after the upgrade to Package Control 2.0 completes (and usually after a restart), several previously-active packages have been moved to the ignored_packages list in Packages/User/Preferences.sublime-settings. I assume that they are moved there temporarily during the upgrade process, whether it is Package Control's itself, or after PC has been installed and it is upgrading in place the packages listed in Packages/Package Control/Package Control.sublime-settings.
Packages/Package Control/Package Control.sublime-settings
I also experienced this when restarting ST2 after I updated PC to 2.0. I also noticed that PC had some errors downloading a few packages. Maybe this prevented updating the ignored_packages afterwards.
Hmm - can't reproduce. Can anyone provide a list of packages this happens with?
This happened again to me this morning with ST2 on XP - I started up with the console open, and watched packages get added to ignored_packages, and I had to remove them manually. I then started ST3, watched a few get added, and then they were removed again, leaving only the original "Vintage" package, so maybe it has something to do with the ST versions?
I didn't make a full list of the ST2 packages moved (sorry), but I remember SublimeREPL, Tag, Neon Theme, and Terminal being among them. Of the 30-odd packages I have, there were probably 10 that got moved today.
I'm pretty sure this is an ST2 issue - I don't think I have had a report of it on ST3.
OK, I can now replicate this on Windows. I made a fresh roaming install of ST 2.0.2, then cloned in my Packages folder that I happened to upload to github (https://github.com/MattDMo/windows-sublime2-packages) last week, so just before the upgrade. I copied over Data/Installed Packages/Package Control.sublime-package and my Data/Settings/License.sublime_license file from my current install location, then fired up the new ST2 and opened the console right away. Sure enough, a bunch of packages were added to ignored_packages, and as they were upgraded they seemed to be removed (in alphabetical order), but at some point the process halted, leaving me with the following:
Data/Installed Packages/Package Control.sublime-package
"Python Flake8 Lint",
"Syntax Highlighting for Sass",
Feel free to clone my repo and see if you can figure this out. I'm at work, so I can't test Mac or Linux at the moment, but I certainly can this evening if that would be helpful.
I just found this error while going back through the console log:
Exception in thread Thread-7:
Traceback (most recent call last):
File ".\threading.py", line 532, in __bootstrap_inner
File ".\threading.py", line 484, in run
File ".\package_control\automatic_upgrader.py", line 198, in do_upgrades
File ".\package_control\package_manager.py", line 454, in install_package
File ".\package_control\package_manager.py", line 223, in list_available_packages
File ".\package_control\package_manager.py", line 157, in list_repositories
File ".\package_control\cache.py", line 84, in merge_cache_under_settings
It was after the most recent item had been upgraded, and removed from ignored_packages, and it seemed to stop the whole process. Let me know if you'd like more context from around the error.
Hi - I experienced the same thing and posted about it on Stack Overflow. It happened a second time this morning, and then again just now when I came back to work. I had restarted my computer in between. These were in ignored_packages in my prefs.
"PHP Zend Framework 2 Helper",
"Emmet Css Snippets",
"Paste PDF Text Block",
I hope that helps!
Same thing happened to me, found out about it here - in my case, Sublime Linter and the Soda Theme (and others) were in my ignored_packages list. (Sorry, I don't have a saved copy of all the entries, didn't know I'd need to save it.)
I believe this is a duplicate of #558 - see that issue for further updates.