.axii/bin folder gets deleted even when only one module is updated

Bug Report

Summary and Bug Description

When only one module or a module and its dependency modules (with either the flag -n and -m respectively) are upgraded, the whole of $ARMARX_WORKSPACE/.axii/bin is deleted at the beginning of the upgrade, which is a problem because then the executables of the modules not upgraded are missing after the upgrade.

Current Behavior

When upgrading the workspace with example axii w ug -m tools/nodejs/16.19 the .axii/bin folder only contains the 3 bins, even if other files were in before.

Expected Behavior

The .axii/bin folder should contain not only the 3 bins of nodejs but also every other file it previously had

Steps to Reproduce

  1. Create new workspace
  2. Activate workspace
  3. Add tools/vs_code/latest to workspace
  4. axii w ug
  5. check content of .axii/bin folder
  6. Add tools/nodejs/16.19 to workspace
  7. axii w ug -m tools/nodejs/16.19
  8. check content of .axii/bin folder
  9. realize only node.js bins are in the folder and the vs_code bin are missing

Diagnosis

Output of axii self report 
┏━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Scope  ┃ Info                                                                ┃
┡━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ Axii   │ Axii 23.12.1.0 @main-0 with shell integration                       │
│ OS     │ Ubuntu 18.04.6 LTS                                                  │
│ Kernel │ Linux 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 │
│        │ UTC 2023 x86_64 GNU/Linux                                           │
│ Shell  │ /bin/bash                                                           │
│ Python │ Python 3.6.9                                                        │
│ Pip    │ certifi==2023.7.22, charset-normalizer==2.0.12, click==8.0.0,       │
│        │ commonmark==0.9.1, cycler==0.11.0, dataclasses==0.8,                │
│        │ dbus-python==1.2.18, decorator==5.1.1, distro==1.7.0, gitdb==4.0.9, │
│        │ GitPython==3.1.18, idna==3.4, igraph==0.9.11,                       │
│        │ importlib-metadata==4.8.3, kiwisolver==1.3.1, matplotlib==3.3.0,    │
│        │ networkx==2.5, notify2==0.3.1, numpy==1.19.0, Pillow==8.4.0,        │
│        │ pkg_resources==0.0.0, psutil==5.9.4, Pygments==2.14.0,              │
│        │ pygraphviz==1.6, pyparsing==3.1.1, PyQt5==5.15.0,                   │
│        │ PyQt5-sip==12.9.1, python-dateutil==2.8.2, python-igraph==0.9.11,   │
│        │ python-Levenshtein==0.12.2, requests==2.26.0, rich==12.6.0,         │
│        │ rich-click==1.2.1, six==1.16.0, smmap==5.0.0, texttable==1.6.7,     │
│        │ thefuzz==0.19.0, typing_extensions==4.1.1, urllib3==1.26.16,        │
│        │ xdg==5.1.1, zipp==3.6.0                                             │
└────────┴─────────────────────────────────────────────────────────────────────┘

More Relevant Logs or Screenshots

This is an example log showing how it currently acts but shouldn't

[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii$ cd bin/
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii/bin$ touch testttttttt
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii/bin$ ls
node-16.18  npm-8.19  npx-8.19  testttttttt
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii/bin$ axii w ug -m tools/vs_code/latest
[...]
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii/bin$ ls
ls: cannot open directory '.': Stale file handle
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii/bin$ cd ..
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii$ ls
bin  config  test
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii$ ls bin/
code  _code
[▽ fluxio] uzivy_duran@pc032:~/fluxio/.axii$