`rust-project.json` generation does not index local or `crate.spec`s into `rust-dependencies`

[Source](https://github.com/Vantle/Vantle)

## Platform Details

| Component | Version | Latest |
|--------------------|--------------|--------|
| **OS** | Windows 11 | ✅ |
| **Bazel Version** | 8.1.1 | ✅ |
| **Rules Rust** | 0.59.2 | ✅ |

## Issue
Since around October of last year (did not bisect issue yet precisely, uncertain if it is a `windows`, `rules_rust`, or `rust-analyzer` issue), the `rust-analyzer` plugin and the `rust-project.json` file generated by Bazel have stopped correctly identifying and indexing dependencies for the Rust project in our repository. Inspecting the file system and `cargo` information manually for issues was not clear for me.

[rust-project.json](https://github.com/user-attachments/files/19527070/rust-project.json)

## Reproduce
1. Plugin load for `rust-analyzer` language service with generated `rust-project json` with `bazel run config=analysis`
2. Observe, `Rust Dependencies` not indexing any crates included in `spec` or local sources files in `Molten` submodule.