refactor(repo-graph): move manifest helpers into module

[t3chn]

Summary

• Move TOML manifest parsing and warning category helpers into a dedicated repo graph manifest module.
• Update Rust, Python, and Node detectors to import manifest helpers from the new module.
• Leave ignored-path detection in the root module for a separate slice.

Issue

• N/A

Test plan

• cargo check
• cargo fmt --check
• git diff --check
• scripts/run-deterministic-tests.sh