bug: asdf-python intercepts mlx_lm.server installation and sets an old python version

### Provide environment information

```bash
I'm pretty confused by how asdf python works. I thought it was just working with python versions, but when I look at all the things in ~/.asdf basically every python command is there from nbdime or mlx_lm.server

I'm confused how I change these version. `asdf set python 3.12` In the new 0.16 does set it properly, but then nbdime then complains since it only has

asdf shimversion nbdime

python 3.12.7
python 3.11.8

So it gives the error

No version is set for command nbdime
Consider adding one of the following versions in your config file at /Users/rich/.asdf/shims/.tool-versions

Do I would have thought that an asdf reship with the python set to another would fix this, but the version seems to never change. How do you now reship these?
```

### To Reproduce

pip install nbdime
asdf shimversion nbdime

python 3.12.7
python 3.11.8

asdf set python 3.12.8
asdf reship

But

asdf shim versions nbdime

Doe snot change it looks like these shims just run "asdf exec nbdime"

### Describe the Bug

The reship does not use the latest version of python. So I'm not clear how I fix this, where is the directory of all the python executables controlled by asdf-python, that's probably where to start :-)

### Expected Behaviour

Well it would be nice to know how to reship with just a single python command. I've tried

asdf reship nbdime 3.12.8

but this doesn't work obviously

Inizia riproducendo il comportamento segnalato con `pip install nbdime`, `asdf shimversion nbdime`, `asdf set python 3.12.8` e `asdf reship`. Leggi la gestione di asdf-python per gli shim e le versioni di Python selezionate, quindi verifica se `asdf shimversion nbdime` riflette la versione selezionata dopo aver ricreato gli shim. Il lavoro è completo quando il comportamento della versione è corretto oppure il workflow di reship supportato è chiaramente stabilito.

Scritto dal modello di indicizzazione a partire dal testo della issue.