Update stale source path references in documentation

[lodyai]

Finding

Several documentation references point to old source file paths that no longer exist.

Evidence:

• docs/netsuke-design.md:895: src/manifest.rs should be src/manifest/mod.rs
• docs/netsuke-design.md:2436: src/runner.rs should be src/runner/mod.rs
• docs/netsuke-design.md:2438: src/runner/process.rs should be src/runner/process/mod.rs
• docs/developers-guide.md:45: src/graph_view/render_html.rs should be src/graph_view/render_html/mod.rs
• docs/rust-testing-with-rstest-fixtures.md:1130: src/fixtures.rs no longer exists

Why This Matters

The documentation is the project knowledge base. Stale paths slow down contributors and make architectural guidance harder to trust.

Proposed Fix

Update the stale references to current module paths or remove obsolete examples where no equivalent path exists.

Acceptance Criteria

• All listed stale paths are corrected or removed.
• docs/contents.md remains accurate if any documentation structure changes.
• make fmt, make markdownlint, and applicable docs gates pass.

[coderabbitai]

🔗 Related PRs

leynos/rstest-bdd#488 - Extend first-party policy hint resolution (9.7.1) [merged]
leynos/memoryd#3 - Record evidence-store engine policy (1.1.1) [merged]
leynos/stilyagi#20 - Refresh agent documentation standards [merged]
leynos/rstest-bdd#502 - E0499/E0502 troubleshooting entry (10.2.2) [merged]
leynos/rstest-bdd#521 - docs: make users-guide links portable outside the repo tree (#499) [merged]

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