[WIN] MSYS2 aliases .pixi/<env_dir>/Libary/bin to .pixi/<env_dir>/Library/usr/bin but different content

[simone-ruffini-kaab]

Conda packages built for windows usually unpack all binaries in <pixi_env_dir>/Libary/bin.
MSYS2 packages (from conda_foge) are a bit different, they unpack binaries in <pixi_env_dir/Libary/usr/bin instead of /bin (makes sense since in linux that is a standard system directory where binaries are found).
BUT: MSYS2 binaries need a root dir that complies with Linux directory tree, so when you run any application (which, make, where, sh) they map the linux / to <pixi_env_dir>/Library/, hence in theory an MSYS utility should see this:

/ -> <pixi_env_dir>/Library
/bin -> <pixi_env_dir>/Library/bin
/usr/bin -> <pixi_env_dir>/Library/usr/bin

Unfortunately this is not what is happening, internally the tools treat /bin as /usr/bin with the following result:

/ -> <pixi_env_dir>/Library
/bin -> <pixi_env_dir>/Library/usr/bin
/usr/bin -> <pixi_env_dir>/Library/usr/bin

This is a huge problem because the two folders in windows are not the same folders and therefore don't have the same content.
The consequence is that conda binaries are usually available in <pixi_env_dir>/Library/bin therefore when I want to access them from make or sh they are not found since these tools look into <pixi_env_dir>/Library/usr/bin.

Hence, my question is how did you solve this?
Did you repackage all your conda packages to unpack in /usr/bin. Did you repackage only MSYS2 packages? What are the options here?

Related question on msys GH