Expected behavior of mj_saveLastXML regarding asset file path:  absolute vs relative?

### Intro

Hi!

I am a PhD student at MIT, using mujoco for dexterous manipulation research. 

I'm curious what's actually the expected behavior of `mj_saveLastXML` regarding the asset file paths;   is it supposed to save with **absolute paths** for all the files, or **relative paths** based on the original XML file that `MjModel` was loaded with (using `from_xml_path`)?    I am observing both behaviors in different scenarios, which I cannot find the pattern of its behavior.

 


### My setup

I'm on macOS using the latest mujoco version (3.3.7) installed via `pip install mujoco` 

### What's happening? What did you expect?

I basically have this directory structure, which I attached as a zip file. 

[saveLastXML_bug.zip](https://github.com/user-attachments/files/23487004/saveLastXML_bug.zip)


```
xmls/
   |_ panda_2f85/
        |_ xxx.obj 
        |_ xxx.obj 
        |_ panda_2f85.xml 
   |_ scene.xml 
```

where `scene.xml` is nothing but an XML model defined with some mocap bodies and ground floors, where the panda model is included using the `<include>` tag. 

```
<mujoco model="panda scene">

  <include file="panda_2f85/panda_2f85.xml"/>

  <worldbody>
    <body name="target" pos="0.5 -0.4 .5" quat="0 1 0 0" mocap="true">
      <geom type="box" size=".02 .02 .02" contype="0" conaffinity="0" rgba=".6 .3 .3 .5"/>
      <site type="sphere" size="0.01" rgba="0 0 1 1" group="1"/>
    </body>
  </worldbody>

</mujoco>
```
Everything loads properly when I load it directly via mujoco GUI. 

**Now, depending on what XML you load, and how you load it, the outcome of `mj_saveLastXML` is different**. 


### Case 1. Load `xmls/panda_2f85/panda_2f85.xml`

```python
model = mujoco.MjModel.from_xml_path(f"xmls/panda_2f85/panda_2f85.xml")
mujoco.mj_saveLastXML("test.xml", model)
with open("test.xml", "r") as f:
    xml_content = f.read()
check_if_file_paths_are_absolute(xml_content)
```

Then `mj_saveLastXML` returns every file path as its relative path. 
```
Number of relative paths : 75
Number of absolute paths : 0
```

### Case 2. Load `xmls/scene.xml` (using relative path) 

```python
model = mujoco.MjModel.from_xml_path("xmls/scene.xml")
mujoco.mj_saveLastXML("test.xml", model)
with open("test.xml", "r") as f:
    xml_content = f.read()
check_if_file_paths_are_absolute(xml_content)
```

Then I cannot load the model;  it parses the asset path in a weird way. 
```
Error opening file 'xmls/xmls/panda_2f85/base.stl': No such file or directory
```


### Case 3. Load `xmls/scene.xml` (using absolute path) 



```python
    model = mujoco.MjModel.from_xml_path(os.path.abspath("xmls/scene.xml"))
    mujoco.mj_saveLastXML("test.xml", model)
    with open("test.xml", "r") as f:
        xml_content = f.read()
    file_paths = check_file_paths(xml_content)
```

Then everything loads properly, and `mj_saveLastXML` writes everything in absolute path. 

```bash
Number of relative paths : 0
Number of absolute paths : 75
```

----

### Expected behavior

For every case above, 

1. `MjModel.from_xml_path` successfully loads the model
2. `mj_saveLastXML` returns an XML with every file path being absolute path. 

### Steps for reproduction

[saveLastXML_bug.zip](https://github.com/user-attachments/files/23487004/saveLastXML_bug.zip)

Unzip the file, and launch 

```bash
pip install mujoco 
python test.py 
```

### Minimal model for reproduction

_No response_

### Code required for reproduction

_No response_

### Confirmations

- [x] I searched the [latest documentation](https://mujoco.readthedocs.io/en/latest/overview.html) thoroughly before posting.
- [x] I searched previous [Issues](https://github.com/google-deepmind/mujoco/issues) and [Discussions](https://github.com/google-deepmind/mujoco/discussions), I am certain this has not been raised before.

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Uh oh!

Expected behavior of mj_saveLastXML regarding asset file path: absolute vs relative? #2941

Intro

My setup

What's happening? What did you expect?

Case 1. Load `xmls/panda_2f85/panda_2f85.xml`

Case 2. Load `xmls/scene.xml` (using relative path)

Case 3. Load `xmls/scene.xml` (using absolute path)