fix(workflow): mark resumed rework as in progress

[big-mon]

Context

Rework issues currently retain that status while the agent works, making resumed execution look like pending feedback.

TL;DR

Move Rework to In Progress when implementation resumes.

Summary

• Verify attached PR targets before reading feedback or updating the workpad from it.
• Record human feedback in the existing workpad before changing the issue state.
• Move the issue to In Progress and read it back before resuming implementation.
• Preserve the bound clone, matching PR and unfinished work.

Alternatives

• Keeping Rework during execution hides whether the agent has resumed work.
• Concurrent manual state edits during kickoff remain outside this change.
• No engine change is needed; the workflow already directs Linear state updates.

Test Plan

• Full env -u __BURRITO ERL_FLAGS='+S 4:4' make -C elixir all: passed; 299 tests, 0 failures, 6 skipped; Dialyzer passed.
• Two default-scheduler runs hit existing retry-timer bounds; rerun with 4 Erlang schedulers, tests unchanged.
• python3 tests/test_repository_workflow.py: 17 tests passed.
• YAML parsing and strict Liquid rendering passed for the canonical and installed workflows.
• git diff --check passed; reviewed feedback capture, state read-back and existing-work preservation.
• Observe a real Rework -> In Progress transition on the next approved rework run.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-24T13:54:15.470215Z	862419c	Manual request

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[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 3500dca0e5

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[big-mon]

[codex] Review follow-up at 862419c:

• Clarified the shared sequence: verify attached PR targets before reading their feedback or changing the workpad from it. The installed workflow is aligned.
• Declined the additional state-recheck guard under the existing operating policy: concurrent manual status changes during kickoff are outside this change, and a second read would not make the mutation atomic. The original thread records the rationale.
• Full local validation passed with 4 Erlang schedulers: 299 tests, 0 failures, 6 skipped; Dialyzer clean. Two default-scheduler runs hit existing retry-timer bounds. Routing tests (17), YAML/Liquid rendering, diff and PR-body checks passed. Live Rework transition remains unverified.

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Swish!

Reviewed commit: 862419c898

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".