conda-env-activate-for-buffer sets PATH to "", causing "ls" "git" "bash" to fail about conda.el HOT 9 OPEN

[masataro ~]$ conda activate pypergame
WARNING: overwriting environment variables set in the machine
overwriting variable {'PKG_CONFIG_PATH', 'LD_LIBRARY_PATH', 'CPATH'}
(pypergame) [masataro ~]$ conda deactivate
[masataro ~]$ conda -V
conda 23.3.1
[masataro ~]$ uname -a
Linux fedora32-T46 6.1.14-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Sun Feb 26 00:31:11 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
[masataro ~]$ emacs --version
GNU Emacs 28.2
Copyright (C) 2022 Free Software Foundation, Inc.
GNU Emacs comes with ABSOLUTELY NO WARRANTY.
You may redistribute copies of GNU Emacs
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING.
[masataro ~]$ env
SHELL=/bin/bash
IMSETTINGS_INTEGRATE_DESKTOP=yes
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1929130,unix/unix:/tmp/.ICE-unix/1929130
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1
HISTCONTROL=ignoreboth
MPI_LIB=/usr/lib64/mpich/lib
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GTK_IM_MODULE=fcitx
CONDA_EXE=/home/masataro/miniconda3/bin/conda
_CE_M=
PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig
HOSTNAME=fedora32-T46
HISTSIZE=1000
TERMCAP=
SSH_AUTH_SOCK=/tmp/ssh-XXXXXXAhSnMu/agent.1929130
HOSTALIASES=/home/masataro/.hostaliases
__MODULES_SHARE_LD_LIBRARY_PATH=:1
INPUT_METHOD=fcitx
INSIDE_EMACS=28.2,comint
XMODIFIERS=@im=fcitx
DESKTOP_SESSION=cinnamon
SSH_AGENT_PID=1929257
EDITOR=emacs
XDG_SEAT=seat0
PWD=/home/masataro
LOGNAME=masataro
XDG_SESSION_DESKTOP=cinnamon
QT_QPA_PLATFORMTHEME=gtk2
XDG_SESSION_TYPE=x11
MODULESHOME=/usr/share/Modules
MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man:/home/masataro/.local/share/man/man1:
MPI_COMPILER=mpich-x86_64
MPI_PYTHON2_SITEARCH=%{python2_sitearch}/mpich
MPI_INCLUDE=/usr/include/mpich-x86_64
CUDA_INCLUDE_DIRS=/usr/include
XAUTHORITY=/run/lightdm/masataro/xauthority
FOAM_TUTORIALS=/usr/share/doc/openfoam-examples/examples
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/masataro
MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich
MPI_HOME=/usr/lib64/mpich
__MODULES_SHARE_MANPATH=:2
HOME=/home/masataro
LANG=ja_JP.UTF-8
LS_COLORS=
XDG_CURRENT_DESKTOP=X-Cinnamon
__MODULES_LMCONFLICT=mpi/mpich-x86_64&mpi
COLUMNS=118
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CUDA_INC_PATH=/usr/include
MPI_SYSCONFIG=/etc/mpich-x86_64
IMSETTINGS_MODULE=fcitx5
MOZ_GMP_PATH=/usr/lib64/mozilla/plugins/gmp-gmpopenh264/system-installed
MPI_SUFFIX=_mpich
XDG_SESSION_CLASS=user
MAKEFLAGS=-j 16
TERM=dumb
_CE_CONDA=
GTK_OVERLAY_SCROLLING=0
LESSOPEN=||/usr/bin/lesspipe.sh %s
USER=masataro
CUDA_ROOT=/usr
MPI_PYTHON_SITEARCH=%{python2_sitearch}/mpich
CONDA_SHLVL=0
MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD
PAM_KWALLET5_LOGIN=/run/user/1000/kwallet5.socket
LOADEDMODULES=mpi/mpich-x86_64
DISPLAY=:0
SHLVL=2
MPI_BIN=/usr/lib64/mpich/bin
QT_IM_MODULE=fcitx
XDG_VTNR=1
DESKTOP_AUTOSTART_ID=105fc95c0f2af207b4168081447244073000019291300017
XDG_SESSION_ID=5
CONDA_PYTHON_EXE=/home/masataro/miniconda3/bin/python
LD_LIBRARY_PATH=/usr/lib64/mpich/lib:/home/masataro/.local/lib:/usr/lib64/:
XDG_RUNTIME_DIR=/run/user/1000
S_COLORS=auto
MPI_PYTHON3_SITEARCH=/usr/lib64/python3.10/site-packages/mpich
DEBUGINFOD_URLS=https://debuginfod.fedoraproject.org/ 
MPI_MAN=/usr/share/man/mpich-x86_64
which_declare=declare -f
KDEDIRS=/usr
GTK3_MODULES=xapp-gtk3-module
XDG_DATA_DIRS=/home/masataro/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/lib64/ccache:/home/masataro/.local/texlive/2019/bin/x86_64-linux:/home/masataro/.roswell/bin:/home/masataro/.local/bin:/home/masataro/bin:/home/masataro/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles
GDMSESSION=cinnamon
_LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
MAIL=/var/spool/mail/masataro
CPATH=/home/masataro/.local/include:/usr/include/:
GIO_LAUNCHED_DESKTOP_FILE_PID=2496497
GIO_LAUNCHED_DESKTOP_FILE=/usr/share/applications/emacs.desktop
MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl
BASH_FUNC_ml%%=() {  module ml "$@"
}
BASH_FUNC_which%%=() {  ( alias;
 eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@
}
BASH_FUNC_module%%=() {  eval `/usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash "$@"`;
 _mlstatus=$?;
 return $_mlstatus
}
BASH_FUNC_bell%%=() {  if [[ $? == 0 ]]; then
 $HOME/.local/bin/bell -s "$@";
 else
 $HOME/.local/bin/bell -f "$@";
 fi
}
_=/usr/bin/env
[masataro ~]$ 

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('$HOME/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then
        . "$HOME/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="$HOME/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

    conda env config vars set LD_LIBRARY_PATH=
    conda env config vars set PYTHONPATH=
    conda env config vars set PKG_CONFIG_PATH=
    conda env config vars set PYTHONHASHSEED=30294 # set for reproducibility:

    # these are required for building dependencies properly under conda
    conda env config vars set CPATH=${CONDA_PREFIX}/include:${CONDA_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/include:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/espen/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/espen/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/espen/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/espen/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

$ cond env list
# conda environments:
#
base                     /home/espen/miniconda3
clinica                  /home/espen/miniconda3/envs/clinica
homl3                 *  /home/espen/miniconda3/envs/homl3
pydata                   /home/espen/miniconda3/envs/pydata


$ cond env config vars list

$ echo $PATH
/home/espen/miniconda3/envs/homl3/bin:/home/espen/miniconda3/condabin:/home/espen/.cargo/bin:/home/espen/.zig:/home/espen/.config/emacs/bin:/home/espen/.local/scripts:/home/espen/.local/bin:/home/espen/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

$ uname -a
Linux forsker-pc 6.2.0-36-generic #37~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct  9 15:34:04 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

$ env
VNCDESKTOP=forsker-pc:2 (espen)
TEXINPUTS=.:/home/espen/.config/emacs/.local/straight/build-29.1/auctex/latex:
CONDA_PROMPT_MODIFIER=(homl3) 
MAIL=/var/mail/espen
LC_TIME=nb_NO.UTF-8
SSH_CLIENT=<redacted>
USER=espen
SSH_AGENT_PID=1055174
XDG_SESSION_TYPE=x11
SHLVL=2
CONDA_SHLVL=2
LESS=-R
MOTD_SHOWN=pam
OLDPWD=/home/espen
HOME=/home/espen
DESKTOP_SESSION=xfce
SSH_TTY=/dev/pts/1
LSCOLORS=Gxfxcxdxbxegedabagacad
ZSH=/home/espen/.oh-my-zsh
HUSHLOGIN=FALSE
PANEL_GDK_CORE_DEVICE_EVENTS=0
OPENAI_API_KEY=<redacted>
_ZSH_TMUX_FIXED_CONFIG=/home/espen/.oh-my-zsh/plugins/tmux/tmux.extra.conf
PAGER=less
LC_MONETARY=nb_NO.UTF-8
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
_CE_M=
LOGNAME=espen
_=/home/espen/.config/emacs/bin/doom
XDG_SESSION_CLASS=user
XDG_SESSION_ID=25
TERM=dumb
_CE_CONDA=
PATH=/home/espen/miniconda3/envs/homl3/bin:/home/espen/miniconda3/condabin:/home/espen/.cargo/bin:/home/espen/.zig:/home/espen/.config/emacs/bin:/home/espen/.local/scripts:/home/espen/.local/bin:/home/espen/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
SESSION_MANAGER=local/forsker-pc:@/tmp/.ICE-unix/1055157,unix/forsker-pc:/tmp/.ICE-unix/1055157
LC_ADDRESS=nb_NO.UTF-8
XDG_MENU_PREFIX=xfce-
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:2.0
REMOTEHOST=<redacted>
LC_TELEPHONE=nb_NO.UTF-8
LANG=en_US.UTF-8
DESKTOP_STARTUP_ID=xfce4-panel/|usr|bin|emacs/1056424-9-forsker-pc_TIME80105680
XDG_CURRENT_DESKTOP=XFCE
ZSH_TMUX_TERM=screen-256color
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
XMODIFIERS=
CONDA_PYTHON_EXE=/home/espen/miniconda3/bin/python
SSH_AUTH_SOCK=/tmp/ssh-XXXXXXlByfKn/agent.1055173
LC_NAME=nb_NO.UTF-8
SHELL=/usr/bin/zsh
CONDA_DEFAULT_ENV=homl3
LC_MEASUREMENT=nb_NO.UTF-8
LC_IDENTIFICATION=nb_NO.UTF-8
PWD=/home/espen/PhD/adni
FZF_DEFAULT_COMMAND=rg --files --hidden --glob "!.git/*"
CONDA_EXE=/home/espen/miniconda3/bin/conda
VIRTUAL_ENV_DISABLE_PROMPT=1
ZSH_TMUX_CONFIG=/home/espen/.tmux.conf
SSH_CONNECTION=<redacted>
XDG_CONFIG_DIRS=/etc/xdg
XDG_DATA_DIRS=/usr/local/share:/usr/share
LC_NUMERIC=nb_NO.UTF-8
CONDA_PREFIX=/home/espen/miniconda3/envs/homl3
LC_PAPER=nb_NO.UTF-8
EDITOR=vim