Updating miniforge appears to result in a corrupted base env (mix of updated codes and old codes)
bugwindows
### Solution to issue cannot be found in the documentation.
- [x] I checked the documentation.
### Issue
I tried to upgrade miniforge (from 25.3.1 to the latest, 25.11.0) using `mamba update --all` in `base` env. (Platform: Windows 11 running in git-bash). The update appears to have left the `base` env in some consistent state, e.g., the python codes for `conda-libmamba-solver` in `site-packages` are a mix of the updated and the old codes.
`conda-libmamba-solver` is not the only package that has the problem. Many other packages have similar issue as well, e.g., `pip`, `requests`, `urllib3`, etc.
### Symptoms:
After the update, when I tried `conda --version`, there were error messages:
```sh
Error while loading conda entry point: conda-libmamba-solver (cannot import name 'Spinner' from 'conda.common.io' (C:\pkg\_winNonPortables\miniforge3\lib\site-packages\conda\common\io.py))
Error while loading conda entry point: conda-libmamba-solver (cannot import name 'Spinner' from 'conda.common.io' (C:\pkg\_winNonPortables\miniforge3\lib\site-packages\conda\common\io.py))
conda 25.11.0
```
`conda` still somewhat works despite the error messages, for the couple read-only commands I tried: list, activate.
For now I dare not try any commands that would change environments. Specifically, I did not rollback either, afraid that it'd cause further corruption.
### Details 1
In the `mamba update` output, there were lots of warnings about files already present in the environment for many packages, e.g., for `conda-libmamba-solver`:
```
Linking conda-libmamba-solver-25.11.0-pyhd8ed1ab_0
warning libmamba [conda-libmamba-solver-25.11.0-pyhd8ed1ab_0] The following files were already pre:
- Lib\site-packages\conda_libmamba_solver\__init__.py
- Lib\site-packages\conda_libmamba_solver\conda_build_exceptions.py
- Lib\site-packages\conda_libmamba_solver\exceptions.py
- Lib\site-packages\conda_libmamba_solver\index.py
- Lib\site-packages\conda_libmamba_solver\mamba_utils.py
- Lib\site-packages\conda_libmamba_solver\plugin.py
- Lib\site-packages\conda_libmamba_solver\repoquery.py
- Lib\site-packages\conda_libmamba_solver\solver.py
- Lib\site-packages\conda_libmamba_solver\state.py
- Lib\site-packages\conda_libmamba_solver\utils.py
Linking conda-25.11.0-py310h5588dad_0
```
When I looked at the actual files in `site-packages/conda_libmamba_solver`, it seems that the files listed in the warnings are the old version (based on timestamp). The directory also have a few files with in new versions, presumably did not exist in the old version.
### Details 2
The version info I got is inconsistent, depending on whether I use `mamba list` or `conda list`
`mamba list` indicates it's the updated 25.11.0
```sh
conda-libmamba-solver 25.11.0 pyhd8ed1ab_0 conda-forge
```
`conda list` indicates it's the old 25.3.0 (from pypi for some reason):
```sh
conda-libmamba-solver 25.3.0 pypi_0 pypi
```
### Installed packages
```shell
# mamba list results
# note: conda list gives conflicting results, as indicated above.
Name Version Build Channel
-----------------------------------------------------------------------------
archspec 0.2.5 pyhd8ed1ab_0 conda-forge
backports.zstd 1.2.0 py310h458dff3_0 conda-forge
boltons 25.0.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.2.0 py310hfff998d_1 conda-forge
bzip2 1.0.8 h0ad9c76_8 conda-forge
ca-certificates 2025.11.12 h4c7d964_0 conda-forge
certifi 2025.11.12 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py310h29418f3_1 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
conda 25.11.0 py310h5588dad_0 conda-forge
conda-libmamba-solver 25.11.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge
conda-package-streaming 0.12.0 pyhd8ed1ab_0 conda-forge
cpp-expected 1.3.1 h477610d_0 conda-forge
distro 1.9.0 pyhd8ed1ab_1 conda-forge
fmt 12.0.0 h29169d4_0 conda-forge
frozendict 2.4.7 py310h29418f3_0 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_1 conda-forge
jsonpointer 3.0.0 pyhcf101f3_3 conda-forge
krb5 1.21.3 hdf4eb48_0 conda-forge
libarchive 3.8.2 gpl_h26aea39_100 conda-forge
libcurl 8.17.0 h43ecb02_0 conda-forge
libexpat 2.7.3 hac47afa_0 conda-forge
libffi 3.5.2 h52bdfb6_0 conda-forge
libiconv 1.18 hc1393d2_2 conda-forge
liblzma 5.8.1 h2466b09_2 conda-forge
liblzma-devel 5.8.1 h2466b09_2 conda-forge
libmamba 2.4.0 h3f46830_1 conda-forge
libmambapy 2.4.0 py310h8a88361_1 conda-forge
libsolv 0.7.35 h8883371_0 conda-forge
libsqlite 3.51.1 hf5d6505_0 conda-forge
libssh2 1.11.1 he619c9f_0 conda-forge
libxml2 2.15.1 h5d26750_0 conda-forge
libxml2-16 2.15.1 h692994f_0 conda-forge
libzlib 1.3.1 h2466b09_2 conda-forge
lz4-c 1.10.0 h2466b09_1 conda-forge
lzo 2.10 h6a83c73_1002 conda-forge
mamba 2.4.0 h794742e_1 conda-forge
menuinst 2.4.1 py310h73ae2b4_0 conda-forge
miniforge_console_shortcut 3.0 h57928b3_0 conda-forge
msgpack-python 1.1.2 py310he9f1925_1 conda-forge
nlohmann_json-abi 3.12.0 h0f90c79_1 conda-forge
openssl 3.6.0 h725018a_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
platformdirs 4.5.1 pyhcf101f3_0 conda-forge
pluggy 1.6.0 pyhf9edf01_1 conda-forge
pybind11-abi 11 hc364b38_1 conda-forge
pycosat 0.6.6 py310h29418f3_3 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pysocks 1.7.1 pyh09c184e_7 conda-forge
python 3.10.19 hc20f281_2_cpython conda-forge
python_abi 3.10 8_cp310 conda-forge
reproc 14.2.5.post0 h2466b09_0 conda-forge
reproc-cpp 14.2.5.post0 he0c23c2_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.18.16 py310h29418f3_0 conda-forge
ruamel.yaml.clib 0.2.14 py310h29418f3_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
simdjson 4.2.2 h49e36cd_0 conda-forge
tk 8.6.13 h2c6b04d_3 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
truststore 0.10.3 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ucrt 10.0.26100.0 h57928b3_0 conda-forge
urllib3 2.6.1 pyhd8ed1ab_0 conda-forge
vc 14.3 h2b53caa_33 conda-forge
vc14_runtime 14.44.35208 h818238b_33 conda-forge
vcomp14 14.44.35208 h818238b_33 conda-forge
vs2015_runtime 14.44.35208 h38c0c73_33 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
win_inet_pton 1.1.0 pyh7428d3b_8 conda-forge
xz 5.8.1 h208afaa_2 conda-forge
xz-tools 5.8.1 h2466b09_2 conda-forge
yaml-cpp 0.8.0 h63175ca_0 conda-forge
zstandard 0.25.0 py310h1637853_1 conda-forge
zstd 1.5.7 h534d264_6 conda-forge
```
### Environment info
```shell
libmamba version : 2.4.0
mamba version : 2.4.0
curl version : libcurl/8.17.0 Schannel zlib/1.3.1 libssh2/1.11.1
libarchive version : libarchive 3.8.2 zlib/1.3.1 liblzma/5.8.1 bz2lib/1.0.8 liblz4/1.10.0 libzd
envs directories : C:\pkg\_winNonPortables\miniforge3\envs
package cache : C:\pkg\_winNonPortables\miniforge3\pkgs
C:\Users\SL\.mamba\pkgs
C:\Users\SL\AppData\Roaming\.mamba\pkgs
environment : base (active)
env location : C:\pkg\_winNonPortables\miniforge3
user config files : C:\Users\SL\.mambarc
populated config files : C:\Users\SL\.condarc
C:\pkg\_winNonPortables\miniforge3\.condarc
virtual packages : __win=10.0.26200=0
__archspec=1=x86_64_v3
__cuda=11.6=0
channels : https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/pytorch/noarch
https://conda.anaconda.org/pytorch/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
base environment : C:\pkg\_winNonPortables\miniforge3
platform : win-64
```
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