doom sync & doom upgrade break Doom Emacs

[pythonian23]

I confirm that...

• [X] I have searched the issue tracker, documentation, FAQ, Discourse, and Google, in case this issue has already been reported/resolved.
• [X] I have read "How to Debug Issues", and will use it to provide as much information about this issue as possible.
• [X] The issue can be reproduced on the latest available commit of Doom.
• [X] The issue can be reproduced on a stable release of Emacs, such as 27, 28, or 29. (Unstable versions end in .50, .60, or .9x)

Expected behavior

After running doom sync and/or doom upgrade, Doom Emacs should function with all of its builtin keybindings working.

Current behavior

After running doom sync and/or doom upgrade, a majority of the default keybindings are unset. For example, SPC b is undefined. doom install, on the other hand, functions normally.

I believe the issue is originating from differences .config/emacs/.local/@/init.29.el, and I've attached the files after doom install and doom init below.

In addition, it seems that M-x doom/reload temporarily fixes the problem (it returns after restarting Emacs)

install.el.txt - .config/emacs/.local/@/init.29.el after doom install; presumably how things should be (all ( replaced with \n( to make diff work) sync.el.txt - .config/emacs/.local/@/init.29.el after doom sync (all ( replaced with \n( to make diff work) i2s.el.diff.txt - diff

Steps to reproduce

1. Run doom sync
2. Open Emacs - broken
3. Run doom install
4. Open Emacs - fixed

M-x doom/info

doom install - https://pastebin.com/44rNqNnx doom sync - https://pastebin.com/tpVbmdXZ

System Information

Above

[pythonian23]

oh god virusman is here too

[gagbo]

oh god virusman is here too

Sorry for that

[hlissner]

Please check the *Messages* buffer for errors at startup. Keybindings are often the first casualty to startup errors. If you find an error, please produce a backtrace from it as well.

[pythonian23]

There aren't errors happening on startup - the message buffer is normal

[hlissner]

I notice that the order of modules is different when you use doom sync, which can easily cause your issue, but I can't reproduce it. Is your config up somewhere I can see it?

[pythonian23]

Here's my doom config: https://github.com/pythonian23/dotfiles/tree/main/.config/doom

[hlissner]

It seems it's doom install that gets the module list backwards. I notice you have :config default very high in your doom!. Order matters for the :config and :app groups (they should be at the bottom), so moving them there should fix your issue as far as doom sync is concerned. Still looking into the discrepancy though.

[pythonian23]

It works again! Thanks :D