doom sync -u deletes $EMACSDIR/bin and leaves Doom in broken state

[liar666]

I confirm that...

• I have searched the issue tracker, documentation, FAQ, Discourse, and Google, in case this issue has already been reported/resolved.
• I have read "How to Debug Issues", and will use it to provide as much information about this issue as possible.
• The issue can be reproduced on the latest available commit of Doom.
• 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

running doom sync -u should work flawlessly

Current behavior

DOOM SYNC IS VERY DANGEROUSLY BROKEN AS IT RECURSIVELY DELETES ../!!!!

Running doom sync -u lead to some master/HEAD errors for some repos. I corrected them by deleting $DOOM_HOME/.local/straight/[build,repos}... then re running doom sync -u, but when I do I get "doom: command not found" & indeed, $DOOM_HOME/bin has desappeared. I had to clone the doom repos then copy paste the files into my $DOOM_HOME after each error!!!

Steps to reproduce

• Running doom sync -u
• Get some master/HEAD errors for some repos (e.g. org-gcal, emacs-calfw...)
• Correct them by deleting $DOOM_HOME/.local/straight/[build,repos}...
• Re running doom sync -u
• Observing that $DOOM_HOME/ contains almost only .local

Example of execution trace:

> Tangling your literate config...
  ✓ Done tangling 1 file(s)!
- Using Emacs 29.3 @ /usr/local/bin/emacs
> Synchronizing "default" profile...
  > Ensuring packages are installed and built...
    > Updating recipe repos...
    > Cloning read-aloud.el...macsmirror-mirror...
    > Building read-aloud...
    > Building tabnine...
    > Building flymake-languagetool...
    > Building keycast...
    ✓ Built 4 package(s)
  > Updating all packages (this may take a while)...
    > Repository "emacs-calfw" has a dirty worktree:
    
       M ../../../../LICENSE
       M ../../../../README.md
       D ../../../../read-aloud.el
      ?? ../../../
      ?? ../../../../bin/
      ?? ../../../../docs/
      ?? ../../../../early-init.el
      ?? ../../../../lisp/
      ?? ../../../../modules/
      ?? ../../../../profiles/
      ?? ../../../../shell.nix
      ?? ../../../../templates/

         1) Abort
         2) Stash changes
         3) Discard changes (Choose this if unsure)

      How to proceed? (1, 2, 3; don't know? Pick 3) 3
      Discard all local changes permanently? (y or n) y
    > In repository "emacs-calfw", remote "origin" has URL
      "https://github.com/gromnitsky/read-aloud.el.git"
    but recipe specifies a URL of
      "https://github.com/kiwanami/emacs-calfw.git"

         1) Abort
         2) Rename remote "origin" to "origin-2", re-create "origin" with correct URL, and fetch
         3) Rename remote "origin" manually, re-create it with correct URL, and fetch
         4) Delete remote "origin", re-create it with correct URL, and fetch (Choose this if unsure)
         5) Delete remote "origin", re-create it with manually set URL, and fetch

      How to proceed? (1, 2, 3, 4, 5; don't know? Pick 4) 4
      Really delete remote "origin"? (y or n) y
    > Repository "emacs-calfw" has a dirty worktree:
    
      ?? ../../../
      ?? ../../../../bin/
      ?? ../../../../docs/
      ?? ../../../../early-init.el
      ?? ../../../../lisp/
      ?? ../../../../modules/
      ?? ../../../../profiles/
      ?? ../../../../shell.nix
      ?? ../../../../templates/

         1) Abort
         2) Stash changes
         3) Discard changes (Choose this if unsure)

      How to proceed? (1, 2, 3; don't know? Pick 3) 

System Information

https://pastebin.com/tq2ERZx9

[hlissner]

1. Is your config up somewhere I can see it?
2. Have you set any of the following envvars anywhere: EMACSDIR, DOOMDIR, or DOOMLOCALDIR?
3. Have you symlinked anything in or around your ~/.emacs.d and ~/.doom.d?
4. Your doom/info says you're on commit c662366 (dated 2017-07-30) of Doom, but no such commit exists in our history, and 2017-07-30 seems so old it can't be right. What commit of Doom are you actually on?