Meta: Prioritise refactoring audit findings

[lodyai]

Goal

Track and prioritise the refactoring and documentation findings from the Rust/router + leta + wyvern audit.

Priority Order

1. Remove dead duplicated source first; it is low risk and reduces search/review noise immediately.
2. Decouple runner process execution from CLI and make stderr routing explicit. These two should be designed together because they touch the same boundary.
3. Fix reporter/timing output injection. This improves testability before deeper status changes.
4. Extract repeated CLI hint scanning. This is a small mechanical refactor with focused tests.
5. Split runner generation from reporting and manifest expansion from telemetry. These are broader architecture cleanups and should follow the boundary work.
6. Repair stale documentation paths and improve Rustdoc examples. Docs path fixes are small, while broad example coverage can be staged.

Blocked By

• Remove stale duplicated command backup module #338
• Decouple runner process execution from Cli #339
• Make subprocess stderr routing an explicit policy #340
• Keep verbose timing output behind an injectable reporter sink #341
• Extract shared raw CLI hint scanning logic #342
• Separate Ninja generation steps from runner reporting #343
• Separate manifest expansion events from transformation logic #344
• Update stale source path references in documentation #345
• Improve Rustdoc examples for public and test-support APIs #346

Finding Issues

• Remove stale duplicated command backup module #338: Remove stale duplicated command backup module
• Decouple runner process execution from Cli #339: Decouple runner process execution from Cli
• Make subprocess stderr routing an explicit policy #340: Make subprocess stderr routing an explicit policy
• Keep verbose timing output behind an injectable reporter sink #341: Keep verbose timing output behind an injectable reporter sink
• Extract shared raw CLI hint scanning logic #342: Extract shared raw CLI hint scanning logic
• Separate Ninja generation steps from runner reporting #343: Separate Ninja generation steps from runner reporting
• Separate manifest expansion events from transformation logic #344: Separate manifest expansion events from transformation logic
• Update stale source path references in documentation #345: Update stale source path references in documentation
• Improve Rustdoc examples for public and test-support APIs #346: Improve Rustdoc examples for public and test-support APIs

Notes

Each issue should be handled as an atomic change with the repository quality gates run before merging. For code changes, use the Makefile targets required by AGENTS.md: make check-fmt, make lint, and make test.

[coderabbitai]

🔗 Related PRs

leynos/podbot#96 - Align Podbot roadmap with GIST structure [merged]
#302 - Overhaul Netsuke CLI documentation contract [merged]
leynos/corbusier#79 - Add joint Rust and node audit gate [merged]
leynos/memoryd#3 - Record evidence-store engine policy (1.1.1) [merged]
leynos/stilyagi#20 - Refresh agent documentation standards [merged]

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[leynos]

All nine audit findings tracked by this meta issue now have draft pull requests, implemented in the recommended priority order. Each PR was gated locally (make check-fmt, make lint, make test) and cleared by coderabbit review --agent with zero findings before being opened.

Disposition map (blocked-by → PR):

1. Dead duplicated source — Remove stale duplicated command backup module #338 → PR Remove stale duplicated command backup module (#338) #348 (remove src/stdlib/command/mod_backup.rs).
2. Runner boundary (designed together) — Decouple runner process execution from Cli #339 → PR Decouple runner process execution from Cli (#339) #371 (NinjaProcessOptions, decouple process layer from Cli); Make subprocess stderr routing an explicit policy #340 → PR Make subprocess stderr routing an explicit policy (#340) #372 (StderrMode policy, stacked on Decouple runner process execution from Cli (#339) #371).
3. Reporter/timing injection — Keep verbose timing output behind an injectable reporter sink #341 → PR Make verbose timing output sink injectable (#341) #373 (injectable TimingSink).
4. CLI hint scanning — Extract shared raw CLI hint scanning logic #342 → PR Extract shared raw CLI hint scanner (#342) #364 (shared scan_raw_hints).
5. Broader architecture cleanups — Separate Ninja generation steps from runner reporting #343 → PR Separate Ninja generation steps from runner reporting (#343) #374 (pure runner::generation steps); Separate manifest expansion events from transformation logic #344 → PR Separate manifest expansion events from transformation (#344) #375 (ExpansionReport/FilteredEntry, expansion telemetry moved to the caller).
6. Documentation — Update stale source path references in documentation #345 → PR Update stale source path references in documentation (#345) #376 (stale source paths); Improve Rustdoc examples for public and test-support APIs #346 → PR Document runner file-IO and glob helpers; add theme example (#346) #382 (runner file-I/O + glob helper Rustdoc, plus a representative # Examples; remaining example coverage staged as follow-up per the issue’s "highest-use first" guidance).

The priority sequencing in this issue was followed: dead code first, then the runner/stderr boundary as a designed pair, then timing injection, the mechanical hint-scanner extraction, the broader generation/expansion separations, and finally the documentation fixes.

Each change is atomic on its own branch. This meta can be closed once the nine PRs merge (a couple are stacked: #340 on #339, and #319 elsewhere followed the same pattern); the checkboxes above can be ticked as each lands.