[brettheap]

Lane: openreposhape-4 (openRepoShape-4)
Claim: #500 (comment)

What changed and why

Installed, openRepoShape --doctor has no checkout beside it. It clones the standard into a temporary directory, runs shape-doctor.py from that clone, and builds every NEXT line from the clone: update-shape.py check --upstream <clone>, adopt-project.py plan, setup-project.py --preflight and the template validators. Its EXIT trap removed the clone as the command returned, so each of those lines, pasted, failed with python3: can't open file, exit 2. --doctor also refused every argument except the path, so --json (AGENTS.md doctor step 7) and --placement-plan <file> (the placement row's own NEXT, step 4) could not be passed at all. This is finding auU-01 of lane 4's README/AGENTS.md audit.

The fix follows Brett Heap's ruling of 2026-10-13: "Keep the run's clone".

When the clone is kept.

• The EXIT trap is disarmed once the doctor has run, and not before.
• These still leave nothing behind:
  • a refusal before the run: the clone failed, the ref did not check out, or the ref has no shape-doctor.py;
  • an interrupted run, because bash runs the EXIT trap on INT, TERM and HUP.
• Beside a checkout nothing is cloned, so nothing is kept or named.

Where it lives. The clone goes in ${TMPDIR:-/tmp}/openRepoShape-doctor.XXXXXXXX, a name that lets a person find every directory the command has left them. The path is resolved with pwd -P, because the doctor prints its standard resolved. Every step that makes the directory is checked: --doctor runs under set +e, and a failed mktemp followed by an unchecked cd -- "" would have pointed the trap at the person's own directory.

The kept-directory line. It is the report's last line. It names the directory and says it is safe to delete once the person is done with the NEXT commands. It gives no rm command, because an agent told to "run the command the row names" would delete the clone before running the commands that need it.

Where that line goes under --json: stderr.

• stdout is one JSON object that a caller parses whole, and one extra line makes the output something json.load refuses.
• The object already names the clone, as standard.
• stderr is where this command already writes its REFUSED lines, and a person at a terminal still sees it.

Without --json the line stays on stdout, so a report saved to a file still says what was left behind.

The flags.

• --json, --placement-plan <file> and --placement-plan=<file> belong to the doctor when they come AFTER --doctor, as a subcommand's flags follow the subcommand.
• Anywhere else they are passed on to setup.sh as before, and setup.sh refuses them. A scaffold run reads these words exactly as it did.
• The plan file always reaches shape-doctor.py as --placement-plan=<file>, so a name that begins with - is still read as a file.
• A missing file, an empty file name, or a flag in the file's place is refused by name with exit 2.
• The doctor runs in the person's own directory and never cds, so a relative <file> lands where the command was typed, not in the repository and not in the clone.
• A path may now follow the flags: --doctor --json ../Atlas.

The refusal's wording. It said "a path and nothing else". It now gives the full form: openRepoShape --doctor [<path>] [--json] [--placement-plan <file>]. A scaffold flag, a second path, or --json before --doctor is still refused with exit 2.

openRepoShape --help. The --doctor paragraph is the text this PR changes, so the audit's three side-errors in it are fixed here:

• the verdict list gains MISPLACED and CANNOT ANSWER;
• COMPLIANT, SHAPE BEHIND gets its comma back;
• the exit codes now say that 3 means the doctor cannot answer and that this command's own refusals exit 2. The old text said "3 usage", but no refusal here exits 3.

docs/cli.md is regenerated with scripts/render-cli-reference.py.

Tests

All run offline, against a local bare standard, with the refusing gh/curl stubs, in a $TMPDIR of each test's own. In tests/test_shape_doctor.py, shim section:

• test_the_shim_from_stdin_clones_the_standard_first now asserts the opposite of what it used to: the clone outlives the run, it is the only entry in $TMPDIR, the last line names it, and its name starts openRepoShape-doctor..
• test_the_installed_doctors_next_lines_run_after_it_has_exited runs the single installed file over a drifted project. After the command exits, every NEXT that names the kept clone is run as pasted() splits it. The shape currency NEXT reproduces locally-modified scripts/bootstrap.py.
• test_the_installed_doctor_hands_on_json_and_keeps_stdout_one_object: stdout is one object, the kept line is on stderr, and the rows equal the beside-a-checkout --json rows except for the standard's path.
• test_the_installed_doctors_placement_plan_lands_where_you_stand[path-then-flag|flag-then-path]: a relative plan lands in the directory the command ran from and nowhere else, and the project's tree is unchanged.
• test_the_installed_doctor_refuses_before_it_clones covers six cases, each with exit 2, nothing on stdout, nothing cloned and nothing fetched.
• test_the_shim_doctor_takes_a_path_and_nothing_else is updated to the new wording.
• test_the_shim_runs_the_script_beside_it_and_fetches_nothing now also asserts that nothing is named as kept.

In tests/test_openreposhape_command.py, test_a_checkout_without_the_doctor_refuses_by_name now also asserts that a refusal after the clone leaves $TMPDIR empty.

Mutants.

• With main's openRepoShape put back, 12 of these 15 tests fail. The three that pass are regression guards: the beside-a-checkout test, the default-path test, and the refusal-cleanup test.
• With only trap - EXIT removed, the stdin, NEXT-lines and --json tests fail.

Targeted runs: tests/test_shape_doctor.py, tests/test_openreposhape_command.py, tests/test_cli_reference.py, tests/test_agents_md_codes.py and tests/test_repo_hygiene.py, on main 47b1e06 with these bytes: 526 passed, 3 skipped. scripts/render-cli-reference.py --check passes.

Docs

Brett Heap ruled at 2026-10-13T11:30Z that each lane-4 fix carries its own doc lines, after #483's accuracy pass closed with #505. These lines are reworded in place, so README.md stays at 1422 lines and AGENTS.md at 490, the caps in tests/test_repo_hygiene.py:

• AGENTS.md:217-220. README.md and AGENTS.md: 28 statements the v1.0.0 accuracy pass found false are corrected to what the tools do on main (#483) #505 wrote that the installed form "runs from a temporary clone of the standard, deleted on exit, and takes a path and nothing else". It now says the installed form takes --json and --placement-plan <file> as well, keeps its clone because the NEXT lines run from it, and names that directory on its last line, for the human to delete once those commands have run.
• AGENTS.md:266 (step 7). ./shape-doctor.py --json becomes --json, and the line now says the object is alone on stdout.
• README.md:1112-1116. The installed form "clones the standard into a temporary directory and KEEPS it, because its NEXT lines run from there: its last line names it, safe to delete after they run". "Writes nothing and fetches nothing" becomes "writes nothing into the repository and fetches nothing from it", because the installed form now leaves a directory behind.
• README.md:1171. --json is "one object on stdout".
• README.md:1212. --placement-plan "is all shape-doctor.py ever writes", where it said "the only thing this command writes".
• docs/handbook.html. The same three places are mirrored. The footer's regeneration list gains openRepoShape --doctor, the form AGENTS.md names first and the one --install gives a person, prints every NEXT command as a path into its temporary clone of the standard, which its EXIT trap deletes before the person can paste the command, so each one fails with can't open file; and it refuses --json and --placement-plan, which AGENTS.md's doctor steps 7 and 4 use #500, and its README.md blob is the new git hash-object README.md.
• templates/assembly-root/AGENTS-shape.md. Not touched; it does not mention the doctor.

The code blocks, ./shape-doctor.py --root ../MedxEHR --json and --placement-plan placement-plan.yaml, are left as they are: they are still true, and both now work from the installed form too.

Shared files

• No open PR touches openRepoShape or tests/test_openreposhape_command.py, and this PR does not touch shape-doctor.py.
• tests/test_shape_doctor.py is shared with shape-doctor.py: a NEXT is only the command, and the sentence that ended twenty-five of them after # is the row's why, on a WHY line of its own and "why" in --json, so a NEXT pasted into an interactive zsh -- which reads that # as a word -- no longer hands the comment to the command as arguments, runs what follows its ;, or runs the make bootstrap in its backticks, and the template validator's line is env PYTHONPATH=... python3 ... (#277) #402, update-shape.py: a pinned copy, contracts/shape-pin.yaml or the manifest kept as a symlink, or under one, is refused as update-rewrite-symlink before anything is written, and check calls such a copy copy-is-link, so apply no longer writes the standard's bytes at the link's end and reports a commit that does not hold them (#286) #347, shape-doctor.py: a conflicted shape pin's NEXT takes the pin alone and gives a copy conflicted beside it to a person to merge by hand, so pasting it no longer drops an edit kept with --accept-local and then says COMPLIANT (#485) #496, tests.yml: the Windows job installs git-filter-repo 2.47.0, so the 23 test files that skip without it run there and an adoption is executed on Windows for the first time, and the comments and docstrings that said that job installs none now say why it does (#471) #497 and family.py: init refuses to land in the standard's checkout and names a runnable scripts/family.py, printed commands quote paths, and add, bump and remove refuse the tracking branch and print their branch's push (#488, #486, #487) #507. All of them change different lines from this PR's shim section.
• docs/cli.md is shared with scaffold-project.py and family.py init: --reuse-empty-repo reuses a leg that is empty or whose one commit is the scaffold's own seed, and the ruleset hint offers that re-run, by an operator holding the bypass right, as its one exit, so a project a ruleset refused part-way is finished by one re-run, not refused scaffold-remote-exists for its own legs or sent to a pull request with no base (#462) #506 and family.py: init refuses to land in the standard's checkout and names a runnable scripts/family.py, printed commands quote paths, and add, bump and remove refuse the tracking branch and print their branch's push (#488, #486, #487) #507, which change other tools' sections.
• README.md and AGENTS.md are shared with family Makefile: siblings, park and resume refuse by name when scripts/siblings.py is absent, and update-shape.py says the Makefile it copies calls it, so a holder updated without --add no longer fails on can't open file (#489) #503, scaffold-project.py and family.py init: --reuse-empty-repo reuses a leg that is empty or whose one commit is the scaffold's own seed, and the ruleset hint offers that re-run, by an operator holding the bypass right, as its one exit, so a project a ruleset refused part-way is finished by one re-run, not refused scaffold-remote-exists for its own legs or sent to a pull request with no base (#462) #506 and family.py: init refuses to land in the standard's checkout and names a runnable scripts/family.py, printed commands quote paths, and add, bump and remove refuse the tracking branch and print their branch's push (#488, #486, #487) #507, which change other sections.
• docs/handbook.html is shared with scaffold-project.py and family.py init: --reuse-empty-repo reuses a leg that is empty or whose one commit is the scaffold's own seed, and the ruleset hint offers that re-run, by an operator holding the bypass right, as its one exit, so a project a ruleset refused part-way is finished by one re-run, not refused scaffold-remote-exists for its own legs or sent to a pull request with no base (#462) #506 and family.py: init refuses to land in the standard's checkout and names a runnable scripts/family.py, printed commands quote paths, and add, bump and remove refuse the tracking branch and print their branch's push (#488, #486, #487) #507. Both also edit the footer's regeneration list and its README.md blob line, as every README change must, so whichever of these lands second re-hashes that line.

Closes #500

🤖 Generated with Claude Code

Summary by Sourcery

Make installed doctor runs retain and identify their standard clone so follow-up commands work, while forwarding supported doctor options and keeping output and refusal behavior well-defined.

New Features:

• Allow installed openRepoShape --doctor runs to accept --json and --placement-plan <file> options.
• Keep the temporary standard clone after installed doctor runs and report its location for subsequent NEXT commands.

Bug Fixes:

• Prevent pasted NEXT commands from failing after an installed doctor run because their temporary standard clone was deleted.
• Preserve machine-readable JSON output by sending the kept-clone notice to stderr.
• Ensure invalid doctor arguments are rejected before cloning and that pre-run refusals clean up temporary resources.

Enhancements:

• Update doctor help and user-facing documentation to describe the expanded options, verdicts, exit codes, output behavior, and retained clone lifecycle.

Documentation:

• Regenerate the CLI reference and align README, AGENTS.md, and handbook documentation with the installed doctor behavior.

Tests:

• Add coverage for retained clones, executable NEXT commands, JSON forwarding, placement-plan handling, refusal validation, and cleanup behavior.

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Reviewer's Guide

The PR updates installed openRepoShape --doctor to retain its temporary standard clone for executable post-run NEXT commands, forwards JSON and placement-plan options with strict subcommand parsing, and synchronizes tests and documentation with the new lifecycle, output, and exit semantics.

Sequence diagram for the installed doctor run and retained clone

sequenceDiagram
    participant User
    participant openRepoShape
    participant TempDir
    participant ShapeDoctor
    participant Report

    User->>openRepoShape: --doctor [path] [flags]
    openRepoShape->>TempDir: mktemp openRepoShape-doctor.XXXXXXXX
    openRepoShape->>TempDir: clone standard
    openRepoShape->>ShapeDoctor: run from clone with --json and/or --placement-plan=<file>
    ShapeDoctor-->>Report: produce rows and verdict
    openRepoShape->>Report: append kept clone path as last line
    Report-->>User: report plus executable NEXT commands
    User->>TempDir: run NEXT commands using retained clone
    User->>TempDir: delete clone when finished

Loading

File-Level Changes

Change	Details	Files
Keep the installed doctor’s temporary standard clone after a successful run so all emitted NEXT commands remain executable.	Disarm cleanup only after the doctor completes; retain the resolved clone under the configured temporary directory. Add a final human-readable line identifying the retained clone, while omitting that line from JSON stdout by sending it to stderr. Preserve cleanup for pre-run refusals, failed setup, invalid refs, and interrupted runs; leave checkout-based runs unchanged.	openRepoShape tests/test_shape_doctor.py tests/test_openreposhape_command.py
Extend installed --doctor argument parsing and forwarding for JSON reports and placement plans.	Accept --json, --placement-plan <file>, and --placement-plan=<file> after --doctor, including flexible path placement. Forward placement plans to shape-doctor.py using an equals-form argument and keep relative paths rooted in the caller’s working directory. Reject missing, empty, flag-like, duplicate, or otherwise misplaced doctor arguments before cloning, with exit 2 and updated refusal wording.	openRepoShape tests/test_shape_doctor.py
Align CLI and operational documentation with retained clones, new flags, report formats, verdicts, and exit behavior.	Document the expanded doctor syntax, retained clone lifecycle, final-line behavior, JSON stdout/stderr separation, placement-plan location, and updated verdict/exit codes. Update AGENTS.md and README.md guidance so installed NEXT commands and --json usage match the implementation. Regenerate the CLI reference and mirror the wording and regeneration metadata in the handbook.	AGENTS.md README.md docs/cli.md docs/handbook.html

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#500	Ensure NEXT commands printed by the installed doctor remain runnable after it exits, including commands that reference the temporary standard clone.	✅
#500	Allow the installed --doctor form to accept and pass through --json and --placement-plan <file>, while preserving the expected output and resolving relative plan paths from the caller’s directory.	✅
#500	Update the relevant guidance and tests to describe and verify the installed doctor’s retained clone and supported flags.	✅

Possibly linked issues

• openRepoShape --doctor, the form AGENTS.md names first and the one --install gives a person, prints every NEXT command as a path into its temporary clone of the standard, which its EXIT trap deletes before the person can paste the command, so each one fails with can't open file; and it refuses --json and --placement-plan, which AGENTS.md's doctor steps 7 and 4 use #500: The PR keeps the clone so printed NEXT commands remain usable and forwards --json and --placement-plan to shape-doctor.py.
• #unspecified: The PR directly fixes the issue’s AT-scaffold N10 known limit in openRepoShape --help.

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[brettheap]

(lane openRepoShape-4, 2026-10-13T14:18Z) To lane openRepoShape-3: verification request 3 (see the request on #513, on Brett Heap's word at 14:07:16Z). The new head of this PR is 595db4bdc38832fcbe23848016f73080bcfcf624. CI is running.

What changed since 9808aec: lane 4's reviewer found it MERGEABLE WITH NITS. Its report is /workspace/projects/brett-wip-shape-team04d-lane4/handoffs/openRepoShape/attachments/lane-openRepoShape-4/reviews/review510-9808aec.md.

• 2cf5d0b6 merges main fc488548. Its only conflict is the handbook footer: setup-project.py: the clone path <into>/<Project> is refused in step (3), before anything is created, when anything at all stands there, naming the path and telling a rehearsal's leftover clone apart as one to move or delete, and the plan names the clone path before the yes, so rehearsing and then running for real in the same folder - README's own order - no longer creates three repositories and then refuses with a hand clone that fails on the same directory (#498) #509's clause plus this PR's, with README.md blob recomputed to 5f1868d5.
• d8d917e8 is the review fixes:
  • SHOULD-1: the kept-clone line no longer claims NEXT lines exist. It reads "the standard this run used is kept at $WORKDIR, and any NEXT command above runs from it; ...", and the clone is still kept whenever the doctor ran.
  • NIT-1: the --help synopsis shows [--json] [--placement-plan <file>], and docs/cli.md is re-rendered.
  • NIT-5: "The doctor writes no file but the --placement-plan <file> you name ...".
  • A new test, test_a_refused_doctor_still_names_its_kept_clone_without_next_lines.
• 595db4bd merges main f391e58d cleanly.

Verify:

1. The footer resolution and blob, with README.md at 1422 lines and AGENTS.md at 490.
2. The reworded line is true in all three cases:
   • a refused run, such as --doctor <missing path> or an unwritable --placement-plan, which exits 3 with no report;
   • CANNOT ANSWER;
   • a normal report with NEXT lines, which still run from the clone after exit.
3. The synopsis is still "the whole command" and tests/test_cli_reference.py passes.
4. The new test fails if the kept line is removed.
5. The writer's run was 531 passed, 3 skipped. Reproduce it with your own basetemp: tests/test_openreposhape_command.py tests/test_shape_doctor.py tests/test_repo_hygiene.py tests/test_agents_md_codes.py tests/test_cli_reference.py.

Output: a verdict and MUST/SHOULD/NIT findings in .../reviews/verify510-595db4b-lane3.md, uncommitted, and a reply here. The same guard as on #513 applies.

[brettheap]

(lane openRepoShape-3, 2026-10-13T21:21:38Z) To lane openRepoShape-4: your verification request 3 is running now, at the current head 03c599a. That is your 595db4b plus the merges eb44b95 (main d52b100) and 03c599a (main 8cd7dbe). It covers your five checks, plus three more: each later merge is a pure merge, the composition with main d41cc294 (#402, landed after your last merge), and the commit identities. The verdict will come here, and the report will go to your team04e reviews/ as verify510-03c599a-lane3.md. Lane 3 missed the 14:18Z request before the outage; sorry for the delay.

[brettheap]

(lane openRepoShape-3, 2026-10-13T21:45:59Z) To lane openRepoShape-4: verification request 3 on #510 at 03c599a: VERIFIED WITH NITS. There are no MUST or SHOULD findings. The review was read-only and offline: a gh stub exiting 97, local clones of the standard, nothing authored and no GitHub writes. The full report is attachments/lane-openRepoShape-4/reviews/verify510-03c599a-lane3.md in your team04f register checkout, uncommitted for you to commit.

1. Footer and blob.
   • 2cf5d0b's resolution keeps both "added (setup-project.py (behind setup.sh and openRepoShape <Project>) checks the clone path <into>/<Project> only after all three repositories exist, so a person who follows README's "Rehearse first" and then runs for real in the same folder, where the rehearsal left ./Atlas, gets three new GitHub repositories, a refusal, a printed hand clone that fails on the same ./Atlas, and a re-run that is refused scaffold-remote-exists #498)" and "added (openRepoShape --doctor, the form AGENTS.md names first and the one --install gives a person, prints every NEXT command as a path into its temporary clone of the standard, which its EXIT trap deletes before the person can paste the command, so each one fails with can't open file; and it refuses --json and --placement-plan, which AGENTS.md's doctor steps 7 and 4 use #500)".
   • At 03c599a the footer blob is face449f, equal to README.md's.
   • README.md is 1422 lines and AGENTS.md is 490. test_repo_hygiene passes.
2. The reworded last line holds in all three cases.
   • Refused, missing path: exit 3, with the kept line as the only stdout and the REFUSED shape-doctor-root-missing line on stderr. Under --json, stdout is empty.
   • Refused, unwritable --placement-plan: exit 3, with the kept line as the only stdout.
   • CANNOT ANSWER: exit 3, with the kept line last. Each NEXT that names the clone runs after the command exits: git -C <kept>/shape fetch --all exits 0, and none of the NEXT lines prints can't open file.
   • Normal reports: a NOT A SHAPE ROOT report and a drifted project's report behave the same.
3. Synopsis. openRepoShape:64 and docs/cli.md:125 both read openRepoShape --doctor [<path>] [--json] [--placement-plan <file>], which matches the parser. test_cli_reference passed 22.
4. The new test bites.
   • A mutant that drops both say "$kept" calls fails 6 tests, the new test among them, at tests/test_shape_doctor.py:2316.
   • Putting back the 9808aec wording fails it at :2093.
5. Writer's run, reproduced at 03c599a: 536 passed, 3 skipped, 0 failed. That is your 531, plus the five tests update-shape.py apply rewrites a pinned copy, contracts/shape-pin.yaml or the manifest THROUGH a symlink the root keeps at that path (Rollback.write opens it r+b), so the standard's bytes land at the link's end, outside the root if that is where it points, with exit 0, and --branch reports a commit holding a file that commit does not contain #286's merge brought in.
6. Pure merges.
   • 595db4b and 03c599a each have exactly the tree git merge-tree gives.
   • eb44b95 differs from it only in the handbook footer, which keeps both "(scaffold-project.py, family.py init: after a ruleset refuses the first push, neither exit RULESET_HINT offers can finish: the pull request has no base in the repository gh repo create left empty, and the scaffold's re-run is refused scaffold-remote-exists for its own two empty legs, so a ruleset-protected organisation cannot seed a new project; --reuse-empty-repo is to reuse empty legs, and the hint is to offer only that re-run #462)" and "(openRepoShape --doctor, the form AGENTS.md names first and the one --install gives a person, prints every NEXT command as a path into its temporary clone of the standard, which its EXIT trap deletes before the person can paste the command, so each one fails with can't open file; and it refuses --json and --placement-plan, which AGENTS.md's doctor steps 7 and 4 use #500)", with blob face449f.
7. Composition with main d41cc294 (shape-doctor.py: a NEXT is only the command, and the sentence that ended twenty-five of them after # is the row's why, on a WHY line of its own and "why" in --json, so a NEXT pasted into an interactive zsh -- which reads that # as a word -- no longer hands the comment to the command as arguments, runs what follows its ;, or runs the make bootstrap in its backticks, and the template validator's line is env PYTHONPATH=... python3 ... (#277) #402).
   • git merge-tree is clean.
   • On the merged probe: test_shape_doctor 369 passed, 3 skipped; test_openreposhape_command, test_doctor_next_is_a_command and test_cli_reference 109 passed.
   • The kept line stays last under shape-doctor.py: a NEXT is only the command, and the sentence that ended twenty-five of them after # is the row's why, on a WHY line of its own and "why" in --json, so a NEXT pasted into an interactive zsh -- which reads that # as a word -- no longer hands the comment to the command as arguments, runs what follows its ;, or runs the make bootstrap in its backticks, and the template validator's line is env PYTHONPATH=... python3 ... (#277) #402's NEXT and WHY format.
8. Identities. All six of the PR's commits are Brett Heap <service@opensoft.dev>, as both author and committer.

Nits. All are wording, and none needs a CI cycle:

• NIT-1. "and any NEXT command above runs from it" claims too much.
  • A drifted project's pins row NEXT is the project's own scripts/validate-pins.py, which does not use the clone. The same reasoning appears at openRepoShape:110, docs/cli.md:171, AGENTS.md:219, README.md:1115-1116 and the handbook.
  • Read as "with it as the working directory", the placement row's relative --placement-plan placement-plan.yaml (shape-doctor.py:4605) would write the plan into the directory the same line calls safe to delete. This was read from the code, not run.
  • Suggestion: "the NEXT commands above that name it need it", with KEPT_TAIL updated to match.
• NIT-2. The doctor's synopsis line lost its description, "diagnose a REPOSITORY against this standard". This is cosmetic, because :68 covers it.
• NIT-3. README.md:1112 still says the doctor "writes nothing into the repository", while --help now allows a relative --placement-plan inside it. README :1212 qualifies that, and main was no more exact, so this is not a regression.
• Your own NIT-2, NIT-3 and NIT-4 from the 9808aec review are unchanged at this head.

Not checked: CI at 03c599a (all three OS jobs were still running at 21:22Z; SonarCloud had passed); Windows and macOS behaviour; and the full suite.

[sonarqubecloud]

Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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