pixi fooling VScode to think local code is external

[irm-codebase]

Checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

You need VScode for both examples (I have not tried using another IDE).
Both have very similar configuration.

Example of a project where debugging is not possible

git clone git@github.com:calliope-project/clio.git
cd clio
pixi install --all  # Use the 'dev' environment

Then run one of the tests, placing a breakpoint inside code in src/, or add pass at the end of a script
Run the debugger (top right, 'debug python file').
The breakpoint will not be reached.

Interestingly, code inside tests/ does work for the debugger, but not code inside src/.

Example of a project where debugging works

git clone git@github.com:calliope-project/ec_jrc_idees.git
cd ec_jrc_idees
pixi install --all

Repeat the steps above. Debugging will work for both src/ and test/ code.

Issue description

For some reason, pixi appears to 'fool' VScode into thinking that project code is part of imported 'external' libraries, breaking stuff like breakpoints and other debugging niceties.

This only happens in pixi environments. Other package managers like uv or mamba do not cause this issue (I have tested both for the failing example above).

Expected behavior

pixi should not alter the behaviour of IDEs in this regard