homebrew upgrade miniforge removed all environments

[sjg2203]

Verification

• I understand that if I ignore these instructions, my issue may be closed without review.
• I have retried my command with --force.
• I ran brew update-reset && brew update and retried my command.
• I ran brew doctor, fixed as many issues as possible and retried my command.
• I have checked the instructions for reporting bugs.
• I made doubly sure this is not a checksum does not match / SHA256 mismatch error (do not open an issue before trying to open a PR to fix first).

Description of issue

I installed miniforge using homebrew a while ago, works like a charm, though today, homebrew decided to upgrade miniforge to the latest version 25.3.1 and deleted all my environments as well as base, which it created again, but empty.
I lost all my environments due to this massive flaw in upgrading miniforge.
I am not the only one who has had this issue; I found people complaining about it since 2019.

Bear in mind that miniforge is already updated to 25.3.1, so running brew update miniforge --verbose --debug won't provide much information.

Command that failed

brew upgrade miniforge

Output of command with --verbose --debug

❯ brew upgrade miniforge --verbose --debug
/opt/homebrew/Library/Homebrew/brew.rb (Formulary::NullLoader): loading miniforge
/opt/homebrew/Library/Homebrew/brew.rb (Formulary::NullLoader): loading miniforge
/opt/homebrew/Library/Homebrew/brew.rb (Formulary::NullLoader): loading miniforge
/opt/homebrew/Library/Homebrew/brew.rb (Cask::CaskLoader::FromAPILoader): loading miniforge

Output of brew doctor and brew config

❯ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  openssl@1.1

Warning: The following casks have the same name as core casks:
  alienator88/cask/pearcleaner
  alienator88/cask/viz
Their taps are in use, so you must use these full names throughout Homebrew.

Warning: The following formulae have the same name as core formulae:
  petere/postgresql/postgresql@11
  petere/postgresql/postgresql@12
  petere/postgresql/postgresql@13
  petere/postgresql/postgresql@14
  petere/postgresql/postgresql@15
  petere/postgresql/postgresql@16
  petere/postgresql/postgresql@17
  rbenv/tap/openssl@1.1
  shivammathur/php/autoconf@2.69
  shivammathur/php/bison@2.7
  shivammathur/php/php
  shivammathur/php/php@8.1
  shivammathur/php/php@8.2
  shivammathur/php/php@8.3
Some of these can be resolved with:
  brew untap petere/postgresql rbenv/tap shivammathur/php

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libDellMonitorSdkLib.dylib
  /usr/local/lib/libcrypto.1.0.0.dylib
  /usr/local/lib/libiprint.1.0.0.dylib
  /usr/local/lib/libssl.1.0.0.dylib
  /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/fakemysql.h
  /usr/local/include/fakepq.h
  /usr/local/include/fakesql.h
  /usr/local/include/itcl.h
  /usr/local/include/itcl2TclOO.h
  /usr/local/include/itclDecls.h
  /usr/local/include/itclInt.h
  /usr/local/include/itclIntDecls.h
  /usr/local/include/itclMigrate2TclCore.h
  /usr/local/include/itclTclIntStubsFcn.h
  /usr/local/include/mysqlStubs.h
  /usr/local/include/odbcStubs.h
  /usr/local/include/pqStubs.h
  /usr/local/include/tcl.h
  /usr/local/include/tclDecls.h
  /usr/local/include/tclOO.h
  /usr/local/include/tclOODecls.h
  /usr/local/include/tclPlatDecls.h
  /usr/local/include/tclThread.h
  /usr/local/include/tclTomMath.h
  /usr/local/include/tclTomMathDecls.h
  /usr/local/include/tdbc.h
  /usr/local/include/tdbcDecls.h
  /usr/local/include/tdbcInt.h
  /usr/local/include/tk.h
  /usr/local/include/tkDecls.h
  /usr/local/include/tkPlatDecls.h

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/tcl.pc
  /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected static libraries:
  /usr/local/lib/libtclstub8.6.a
  /usr/local/lib/libtkstub8.6.a
brew config


❯ brew config
HOMEBREW_VERSION: 4.5.13-85-g9e4beda
ORIGIN: https://github.com/Homebrew/brew
HEAD: 9e4bedad2fcf40374868fc4a0eab0e57fbdb33cd
Last commit: 17 hours ago
Branch: main
Core tap HEAD: 72209473712d1c66f718ebe42ffcba383f58cec7
Core tap last commit: 6 hours ago
Core tap JSON: 04 Aug 08:56 UTC
Core cask tap JSON: 04 Aug 08:56 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: nano
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.4.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.4.5/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 17.0.0 build 1700
Git: 2.50.1 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.5-arm64
CLT: 16.4.0.0.1.1747106510
Xcode: 16.4
Rosetta 2: false

Output of brew tap

❯ brew tap
alienator88/cask
homebrew/core
petere/postgresql
rbenv/tap
shivammathur/php

[daeho-ro]

Can you guide us how do we correctly handle this situation?

  installer script: {
    executable: "Miniforge3-#{version}-MacOSX-#{arch}.sh",
    args:       ["-b", "-p", "#{caskroom_path}/base"],
  }
  binary "#{caskroom_path}/base/condabin/conda"
  binary "#{caskroom_path}/base/condabin/mamba"

  uninstall delete: "#{caskroom_path}/base"

  zap trash: [
    "~/.conda",
    "~/.condarc",
  ]

During the upgrade, uninstall process remove the base folder and so every single file in that folder may gone. If you do not want to remove them all, please explain what path should remain and deleted. Or you can submit some PR to fix yourself.