Fix infinite loop when messages in the same proto file reference each other

[zhihuizhang17]

Description

Issue
When two messages are defined in the same proto file and reference each other, describing one of them triggers an infinite loop.

Root Cause
Currently, the implementation generates separate description files per message instead of per proto file. This leads to circular references when messages within the same file point to each other.

Proposed Solution
Respect the actual proto file structure:

• Each proto file should correspond to exactly one description file.
• All messages defined in the same proto file should be grouped under that single description file.

This change will prevent recursive loops and ensure consistency with how proto files are organized.

[mjheilmann]

Thanks for opening this issue, but a single sentence followed by promoting a stale draft PR is less than I was hoping for.

Please try to address the following so we can move forward:

1. Describe the issue as fully as you can. This does not require a root cause, but definitely should include the high-level behavior and what a user could experience. i.e. Does it happen on the latest release? Is it a problem when build is running or post-build when the client is calling against the build state? Is it on proto2 or proto3?
2. Ensure your PR has tests that cover the raised issue. Our current pattern is to create the Protos within the codebase for direct usage in tests, so it would demonstrate the Protos that trigger the behavior directly.
3. Ensure your PR is up to date with the current state of the project, and remove the draft label to be considered. In open source it is normal for a PR to be consumable and to be accepted and merged directly as a collaborative effort.
4. Review and clean your code. Lines like # New: <...>, enhance_with_file_based_descriptors, and # Legacy per-message filename mapping to new file-based are related to your AI prompt and do not carry value in the PR or codebase. We can see what is new/changed directly in the changed files.

[mjheilmann]

Here is an alternate solution

The problem is that we weren't checking for the symbol in the state structure before discovering further dependencies, this made the discovery behave like a depth-first search -- which is terrible for recursive structures. I added a proto file that demonstrated this infinite recursion problem, wrote a test that recursed infinitely, then corrected it by adding that check.

@zhihuizhang17 and @PragTob, would you mind looking at this branch and seeing if I successfully recreated and solved your issues? I didn't have enough information to know if what I corrected was the same behavior you described.

[mjheilmann]

This is clearly an issue that we've identified, with the radio silence I'm going to assume that this is the raised issue and will merge my fix and close this issue in roughly a week. This lets this issue resolve while allowing time for any interactions here.

[zhihuizhang17]

closed due to #61