Harness: apply's refusals, the identity port and a Role's writes (#194, PR 2) by don-petry · Pull Request #319 · combsmith/software-factory

don-petry · 2026-10-22T18:03:03Z

Part of "Harness: run and apply for the review Intent, and the model holds no credential that can write" (#194), its second pull request. Record 0054.

What it does

harness/apply.py decides what the apply job does with one Result. It is pure code that is handed the item read again, the run records and the context.

What it holds a Result to. The Decision that admitted its Run, and the Role's manifest. The Result is taken by the digest run reported.
A change under the Run writes nothing, and the Run is superseded. In this order, each with its own code:
- the item is closed;
- its content moved;
- the Factory is paused, or its Pause is unreadable;
- the item is held;
- the Kernel, asked again, no longer admits this Run's Intent on this content. This Run is left out of the Runs, out of those counted active and, by its own GITHUB_RUN_ID, out of those listed before their name.
A Result that may not be written writes nothing. Each case has its own code, and the fault is the Role's (item) unless the Engine failed or the rubric is unreadable:
- it is not this Run's, did not complete, or is uncovered;
- it asks for an Effect the Task does not permit, or names one twice;
- it acts on a thread off the item;
- it posts a Finding other than once, or a non-gating one on a thread, a gating one as an annotation, or one with no place;
- it gives a Disposition other than one half, on a Finding the Task does not list, or the half its Role may not make;
- it resolves a security thread on declined or deferred.
What it decides in a write.
- A review is always a comment on the admitted commit, never an approval.
- A check run's name, conclusion and external_id are apply's.
What it claims. An Effect is claimed only with the key it was read back by. Each posted Finding is written whole as finding/1 from where it was read back.
The job mints nothing for a refused Result, revokes the token whatever happens, and sends nothing after a credential GitHub refused.

adapters/identity.py handles the Role App's token:

It signs the App's JWT with openssl, the key handed through a pipe (/dev/fd/N) and never a file.
It narrows the token to the permissions the Effects' needs name, each within the App's grant.
It holds GitHub's answer to one repo and exactly what was asked, and keeps the token out of every repr and error.
It revokes the token only on GitHub's 204.

The Role writes in adapters/effects.py sit beside the Controller's dispatches from #317. A review, a check run, a thread's resolution and a comment on the item:

each goes through Allowed, held by role_permits(item) to that one item;
each is sent once and recovered by its key: this App's review on this commit, the check run's external_id, the thread's resolved flag, or this App's comments since the Run began, by order and never by text;
each is claimed only as GitHub reads it back.

apply keeps applied/1 as its record (decision 0039); written/1 stays the Controller's. The #19 session agreed.

Rows re-pointed. Every row that waited on harness/apply.py or adapters/identity.py now names the test that holds it, or the narrower planned file that will: harness/push.py for the fix Intent's push, adapters/contract.py, adapters/applied.py for the threads' join, adapters/settings.py for a credential's age, and run.yml for the step.

What waits

The apply step itself. Its command, its live re-read through the facts and records ports, and that re-read's credential belong to "Workflows: the frozen entry shim, the poller, the Run's three jobs and the nudge, each held to its shape" (Workflows: the frozen entry shim, the poller, the Run's three jobs and the nudge, each held to its shape #196). They need the Bot accounts the poller's reads need too.
The check run's grant. effect:create_check_run waits until the Maintainer registers it. Until then a Result asking for a check run ends environment, effect_not_grantable, and test_the_role_app_is_granted_checks_to_write_its_check_run is pending.
A reply on a thread is not built yet.

For the Maintainer: registering `checks: write` on combsmith-sf-pr-review

In the org's settings, open Developer settings, then GitHub Apps, then combsmith-sf-pr-review, then Permissions & events. Under Repository permissions, set Checks: Read and write. Leave every other permission as it is, and keep no events subscribed. Save.
Under Installed GitHub Apps, open combsmith-sf-pr-review and accept the new permission request. Its installation keeps Only select repositories: software-factory and software-factory-canary.
Run trial P-39 again (tools/trial_p39_reach.sh), so its fixture records the registration and installation with checks: write.
Then, in one pull request:
- config/apps.json's need effect:create_check_run becomes {"permission": "checks", "level": "write"};
- pr-review's permissions gain "checks": {"level": "write", "needs": ["effect:create_check_run"]};
- @pending comes off the test above, and the test gets its mutant.

Checks

21 tests in tests/test_apply.py.

Since it opened, apply re-reads with pr-review's own token, read-only, for the needs READS names (the Maintainer, 2026-10-22). The App's grants wait on his sitting, and the test of the live grant is pending.

Gate	Found	Now
Security pass	Nothing at confidence 8 or above	—
Claude review	A retried comment posted twice or claimed another's	Recovered by its place among the item's comments alone, and none sent after one not written
Claude review	A thread resolved with no Disposition skipped every authority check	Only the category's owner resolves, on its own acceptance in the same Result
Claude review	A token minted wider than asked was never revoked; a null repository list crashed `mint`	Revoked before the refusal; every answer that is not one is a refusal
Claude review	The allowlist did not pin a check run's name and commit, or a resolution to the item's threads	Pinned
Claude review	Guards no test held	Each has its test and mutant
Argon	An unreadable count of active Runs (`True`, `-1`) was read as 0, and admitted	Left as read; the Kernel defers
Argon	A comment while its Run is unnamed had no start	Its run's creation, from the unidentified list
Argon	Threads with no comment number, or a count that disagrees, were claimed or crashed	Refused; `sent`
Argon	A check run read back in progress, renamed or with another conclusion was claimed	Each is read back
Muse	Two reviews in one Result were recovered as one (blocker)	Refused, `review_twice`
Muse	A `security` thread could be resolved on the owner's word, though the author's proposal it must rest on is in another Run's Result	A `security` thread is resolved by no Role until the fix Intent brings that proposal (`security_proposal_unread`)
Muse	A grant of no level crashed the narrowing	Refused
Codex	An unconfirmed revocation, a 401 or 403 on a read, a comment edited since the Run began, a whole-file Finding, and a comment with no Run start	Each fixed, with its test
Codex	The allowlist did not pin a review's commit, or a check run's conclusion and key	Pinned
CodeRabbit	Run ids compared as different types	Compared as text

Mutants: 153, every one hand-checked killed. make verify on an export is green.

🤖 Generated with Claude Code

The first commit of harness/. harness/task.py builds task/1 from the pass record's Decision, found by the Run id the Controller minted beside it, the item's facts, the texts read for it, the Role's manifest and the configuration, and refuses a Run no Decision admitted. Each text's trust class is read from who wrote it, never from the text, and a Task says in an optional omitted field what it left out and how much (L-56). harness/engine.py runs the CLI as the P-13 trial does: at the pinned version, read before and after the call; in an empty directory with nothing on its input; with no tool (--tools ""); in an environment of exactly the named variables, CLAUDE_CODE_SUBPROCESS_ENV_SCRUB=1 set and the credential under CLAUDE_CODE_OAUTH_TOKEN alone (issue 287); with result/1 handed resolved and narrowed. Of the answer only structured_output and the counts are read; one that does not validate is a failed Result, result_invalid. harness/run.py writes result.json and its digest, and the log carries the digest alone. New: config/harness.json (harness/1), the Engine's pin, model, each tier's limits, the Task's characters and the advisory reviewers; task/1's optional omitted. Decision record for #194, numbered at enqueue. The 60 rows waiting on harness/ name their tests or the narrower file that will hold them. 39 mutants. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…dispatches sent through the workflow token alone (#193) The first part of #193 PR 2, by the rulings posted on #193 (comment 6329636459): - controller/writes.py plans writes/1 from what the pass returned, in the order they are sent - adapters/effects.py holds the plan to its pass record before anything is sent, sends each dispatch through the pass job's own token's transport, which may send nothing but the three dispatches, and records written/1 - writes/1 and written/1, with examples and counter-examples; controller/1 gains home and the workflows by kind - decision 0049 (numbered at enqueue); 0003's dequeue row, L-48 and L-50 re-pointed; records.py names the dispatcher The status on the item, the dequeue, the tracking issue and the Pause read again wait on P-12, P-2 and new grants. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…urity pass, Argon and Muse A text is budgeted as the Task carries it, escaped, so that the one argument the CLI is given stays under Linux's 128 KiB, and a Task too long for it is refused before the CLI starts, task_too_large; a CLI that cannot be started is a failed Result, never a job that ends with none. Every input is held to its schema and facts read short are refused, so nothing read crashes the job. The Maintainer's texts are kept first, then each trust class in turn. The CLI's own is_error is read beside its exit, as P-13 held it. The machine user is a Role only by the approver's name; a cost that is no finite number is null; the CLI's options and DISABLE_AUTOUPDATER are held word for word. The log test now reaches the stand-in CLI, and an issue's Run, the tier, the CLI's input and each kind's omissions have cases. 60 mutants, each killed by hand the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

# Conflicts: # config/hooks.json # tools/mutants.py

harness/ is verify's input and, since #140, pr-review's own. The stop lists a path once, by its first entry, so both entries carry the same description. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… dispatch's body held, written/1 always left (#193) The Claude review and Argon's read: - the port rebuilds the writes the record's Decisions call for, an approval's under the owner Role, and the plan must be exactly them, in order; only a last successor, which carries nothing, is not in the record - the workflow token's transport holds each dispatch's body: the home branch, a Run's three inputs, none for the poller - the configuration is validated; a refused plan or an unreadable token still leaves written.json and fails the step - a dispatch is counted sent once; 0049, L-50 and adapters/AGENTS.md say only what is held, with two pending tests Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…03 ends the token; no send without a folder (#193) Muse's read of the first head; its approval-role, omission and invented-act findings were already closed by the record's rebuild. - pass/1 gains an optional successor, set by the pass; a plan's successor must agree with it - a 403 ends every later write on the token, as a 401 does, tested - the step checks its output folder before it sends anything Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…ns in (#194, PR 1) SonarCloud's gate on #304 read the job's arguments as a path traversal (S8707, S2083), and the name of the credential's variable as a secret (S6418). Each path the job is given is now followed to where it really is, as tools/eval_result.py does, and one outside the directory the job runs in, a link out among them, is refused before anything is opened, naming no path. The constant holding the credential's name is CREDENTIAL_NAME. A case and a mutant for the refusal. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…into harness/run-task # Conflicts: # adapters/AGENTS.md # docs/decisions/0015-a-lens-is-read-from-its-own-app-and-only-what-gates-holds-a-merge.md # docs/decisions/0018-a-lens-is-read-from-its-own-app-and-workflow-and-only-what-gates-holds-a-merge.md

… PR 1) #298 takes 0048 and #302 takes 0049, so this record is 0050; #304 enqueues once #302 has merged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…298 (0048), #302 (0049) and #304 (0050) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… the trial's (#194, PR 1) CodeRabbit's read: config/harness.json sets the Engine's pin, the limits and which reviewers' text is advisory, so a change to it is a change to what the review is given, and it joins pr-review's own inputs beside the rubric. A test holds its CLI version to the pin tools/trial_p13_cli.sh ran at. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…into harness/run-task # Conflicts: # docs/decisions/0020-a-change-to-the-factorys-own-rules-or-a-lenss-inputs-is-reviewed-by-a-model-lens.md

…t admitted (#194 addendum) The model runs with no tool, so a review Run could not see what it judges (found by the eval job, issue 309). A pull request's Task now carries its diff as its first text: id diff:<content hex>, trust outside whoever pushed it, the last pusher as its source. The run job takes the diff's bytes as a new DIFF argument, held inside its directory, and builds no Task unless their sha256 is the content id the Decision admitted; a pull request with no diff, or one that is not UTF-8, has none, an issue is given none, and no read text may be of kind diff. The change has a budget of its own, config/harness.json's texts.diff_characters (60000), counted escaped. Over it, it is cut at a diff --git line, never inside a file, and omitted says for kind diff how many files and characters were left out. Both budgets full fit the CLI's one argument. Record 0050 gains the change's rows, and the credential moves to an org-level secret the run step alone names, as the Maintainer ruled on 2026-10-22. The scrub is set only with no tool: P-50 found that on a Linux runner, with CLAUDE_CODE_SUBPROCESS_ENV_SCRUB=1 on, a write outside the work directory landed (issue 312). The Engine never starts the CLI with the scrub unless it passes --tools "" once and given nothing; a call that would is failed, engine_failed, before the CLI starts. Record 0050 says so, and that check_workflows holds the run step to it, waiting on run.yml. Eighteen mutants, one per rule, each hand-checked the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… by their titles - The findings a Task is given must be a list, and are carried; a text's writer is held to the facts' actor whole, its name to what task/1 can carry, and its id matched whole, so a text left out is held as one kept is. - A test holds each trust class kept before the next. - The CLI's output that is not UTF-8 is read with what it cannot say replaced, so it is no answer rather than a stopped job. - An OUT that exists, or is a link to nowhere, is refused once, before any path is followed. - Nothing spent is a count of 0.0. - Record 0050 names issues 309 and 312 by their titles. Nine mutants, one per rule, and the OUT mutant moved to the one check left; all 88 Harness mutants hand-checked the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…s/ exists Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… none (P-51) P-51 (issue 312) settles P-50: on a Linux runner at 2.1.306, with CLAUDE_CODE_SUBPROCESS_ENV_SCRUB=1, a sandboxed tool wrote anywhere the runner's user can, in both orders; unset or 0, all four writes were refused. Without the scrub a tool is handed the credential (P-26). So at this pin a Run with any tool cannot both hide the credential and hold its writes: every Run is given no tool, which replaces "no tool for a Run that reads untrusted text". check_workflows will refuse a run, eval or approve step that sets the scrub without --tools "", and any step holding the model credential that passes a tool list; that check waits on run.yml. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…194, PR 2) harness/apply.py decides what the apply job does with one Result, as pure code that is handed the item read again, the run records and the context: - It writes nothing, and the Run is superseded, when the item is closed, its content moved, the Factory paused or the item held, or the Kernel, asked again with this Run left out of the Runs, of those counted active and of those listed before their name, does not admit this Run's Intent on this content. - It writes nothing for a Result that is not the Run's or the Release's, did not complete, or is uncovered (decision 0049). - It writes nothing for a Result that asks for an Effect the Task does not permit, names one twice or acts on a thread off the item, or posts a raised Finding other than once, a non-gating one on a thread, a gating one as an annotation, or one with no place. - A Disposition must give one half, the one its Role may make, on a Finding the Task lists, and a security thread is never resolved on declined or deferred. - A review is a comment on the admitted commit. A check run's name, conclusion and key are apply's. An Effect is claimed only with the key it was read back by, and each posted Finding is written whole as finding/1, its id from its source and its surface. - The job takes the Result by the digest run reported, mints nothing for a refused Result, and revokes the token whatever happens. adapters/identity.py signs the App's JWT with openssl, the key handed through /dev/fd and never a file. It narrows a token to the permissions its Effects need within the App's grant, holds GitHub's answer to one repo and exactly what was asked, keeps the token out of every repr and error, and revokes it only on a 204. Every row waiting on harness/apply.py or adapters/identity.py is re-pointed to a test that holds it, or to the narrower planned file that will: harness/push.py for the fix Intent's push, adapters/contract.py, adapters/applied.py for the threads' join, adapters/settings.py for a credential's age, and run.yml for the job's steps. 72 mutants, each hand-checked the CI way. The live wiring of the job, its record, and the check run's grant wait on the orchestrator's rulings. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…ts pass check_repo Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…n finds none Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

# Conflicts: # adapters/AGENTS.md # docs/decisions/0004-one-run-contract-and-a-job-is-a-credential-boundary.md # docs/decisions/0005-each-role-writes-through-its-own-app.md # docs/decisions/0007-an-approval-is-bound-to-content.md # docs/decisions/0012-lenses-report-findings-and-the-kernel-decides-convergence.md # docs/decisions/0015-a-lens-is-read-from-its-own-app-and-only-what-gates-holds-a-merge.md # docs/decisions/0018-a-lens-is-read-from-its-own-app-and-workflow-and-only-what-gates-holds-a-merge.md # docs/decisions/0020-a-change-to-the-factorys-own-rules-or-a-lenss-inputs-is-reviewed-by-a-model-lens.md # docs/decisions/0022-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md # docs/decisions/0025-acceptance-is-read-from-its-reporter-against-the-contract-a-person-approved.md # docs/decisions/0026-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md # docs/decisions/0029-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported.md # docs/decisions/0036-a-run-listed-before-its-name-is-unidentified-and-defers-every-admission.md # docs/decisions/0038-a-result-asks-and-names-no-one-and-apply-writes-the-finding-it-posted.md # docs/decisions/0039-one-envelope-on-what-crosses-a-boundary-whole.md # docs/decisions/0049-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported-and-one-that-ran-and-left-no-outcome-is-an-attempt.md # docs/decisions/0050-the-model-is-given-a-task-and-no-tool-and-apply-writes-only-what-it-reads-back.md # docs/lessons.md # docs/standards/security-boundaries.md # harness/AGENTS.md # tools/mutants.py

…/apply # Conflicts: # adapters/AGENTS.md # tools/mutants.py

…imed only as read back (#194, PR 2) adapters/effects.py gains the Role writes apply makes, beside the Controller's dispatches: - A review is recovered as one by this App on this commit, else submitted once as a comment, and read back by its id: on the commit, by this App, COMMENTED, with each comment's thread in the order the comments were asked. - A thread's resolution is recovered by its resolved flag. It is refused for a thread on another item, and read back resolved. - A comment on the item is recovered by this App's comments since the Run began, by order and never by text, and read back by its id. A reply on a thread is not built yet and fails. - A 401 or 403 is refused, token_refused, and ends every later write on the credential. No answer or a 5xx is write_unanswered. A write GitHub took but did not read back is sent, and nothing is claimed for it. role_permits(item) lists, for Allowed, only those writes and their reads, on one item; Allowed takes patterns for a path that carries an id read back, matched whole. apply carries a comment's recovery facts, records a port's refusal as refused, and sends nothing after a credential GitHub would not take. 32 mutants, two re-pointed, each hand-checked the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

# Conflicts: # adapters/AGENTS.md # adapters/effects.py # tests/test_effects.py # tools/mutants.py

…anted checks (#194, PR 2) The Maintainer grants combsmith-sf-pr-review checks: write (2026-10-22). Until the registration changes and trial P-39 reads it again, config/apps.json's need effect:create_check_run waits, so no token is minted for a check run, and the test of the grant is pending. The port writes a check run as a Role's: recovered by its external_id, the Run's and the Effect's, on the commit, by this App; else made once, completed, with its annotations, a minor Finding a warning and an info one a notice. It is read back by its id, by this App, on the commit, with as many annotations as were asked, and each annotation's surface is the check run's key and the Finding's ref. More than fifty annotations are refused before anything is sent. 13 mutants, each hand-checked the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

… them, and claims only what it reads back The record of #194's PR 2: what a Result is held to, the change under the Run, the Results that may not be written, what apply decides in a write, the token, the writes through the effects port, what is claimed, the check run's grant, and what waits: the apply step and its live re-read with the workflows story (issue 196), and a Role's push with the fix Intent. Each boundary names its test. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…a wait Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

coderabbitai · 2026-10-22T18:03:13Z

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Reviewing files that changed from the base of the PR and between 57e1554 and 2eff739.

📒 Files selected for processing: 39

adapters/AGENTS.md
adapters/effects.py
adapters/identity.py
config/apps.json
docs/architecture/software-factory-design.md
docs/decisions/0004-one-run-contract-and-a-job-is-a-credential-boundary.md
docs/decisions/0005-each-role-writes-through-its-own-app.md
docs/decisions/0007-an-approval-is-bound-to-content.md
docs/decisions/0012-lenses-report-findings-and-the-kernel-decides-convergence.md
docs/decisions/0015-a-lens-is-read-from-its-own-app-and-only-what-gates-holds-a-merge.md
docs/decisions/0018-a-lens-is-read-from-its-own-app-and-workflow-and-only-what-gates-holds-a-merge.md
docs/decisions/0020-a-change-to-the-factorys-own-rules-or-a-lenss-inputs-is-reviewed-by-a-model-lens.md
docs/decisions/0022-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md
docs/decisions/0025-acceptance-is-read-from-its-reporter-against-the-contract-a-person-approved.md
docs/decisions/0026-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md
docs/decisions/0029-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported.md
docs/decisions/0036-a-run-listed-before-its-name-is-unidentified-and-defers-every-admission.md
docs/decisions/0038-a-result-asks-and-names-no-one-and-apply-writes-the-finding-it-posted.md
docs/decisions/0039-one-envelope-on-what-crosses-a-boundary-whole.md
docs/decisions/0049-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported-and-one-that-ran-and-left-no-outcome-is-an-attempt.md
docs/decisions/0050-the-model-is-given-a-task-and-no-tool-and-apply-writes-only-what-it-reads-back.md
docs/decisions/0054-apply-writes-a-roles-effects-with-a-token-narrowed-to-them-and-claims-only-what-it-reads-back.md
docs/lessons.md
docs/standards/security-boundaries.md
examples/invalid/apps.a-key-in-an-environment-no-job-holds.json
examples/invalid/apps.a-name-without-the-prefix.json
examples/invalid/apps.a-need-not-in-the-table.json
examples/invalid/apps.a-need-the-table-leaves-out.json
examples/invalid/apps.a-permission-github-does-not-have.json
examples/invalid/apps.a-permission-with-no-need.json
examples/invalid/apps.a-repo-not-named-for-slice-0.json
examples/invalid/apps.admin-is-not-a-level.json
examples/invalid/apps.installed-across-the-org.json
harness/AGENTS.md
harness/apply.py
schemas/apps.schema.json
tests/AGENTS.md
tests/test_apply.py
tools/mutants.py

📝 Walkthrough

This pull request adds an apply job that validates Results and admission state, uses repository-scoped Role App tokens for permitted GitHub writes, and records Effects and Findings from verified read-back. It also adds the check-run permission need and updates related tests and documentation.

Changes: Role-scoped apply flow

Layer / File(s)	Summary
Mint Role-scoped installation tokens `adapters/identity.py`, `config/apps.json`, `schemas/apps.schema.json`, `examples/invalid/*`, `tests/test_apply.py`	The identity adapter signs App JWTs, derives permissions from Effect needs, and mints repository-selected installation tokens. It checks returned token permissions and repository scope, supports revocation, and conceals token values in representations. The App schema and configuration add the check-run Effect need.
Constrain and verify Role writes `adapters/effects.py`, `tests/test_apply.py`, `tools/mutants.py`	The effects adapter restricts requests to a selected item and supported write shapes. It handles reviews, check runs, thread resolution, and item comments. It recovers existing writes where specified and reports an Effect as applied only after read-back verification.
Validate Results and record confirmed Effects `harness/apply.py`, `tests/test_apply.py`, `tools/mutants.py`, `harness/AGENTS.md`, `tests/AGENTS.md`, `docs/architecture/`, `docs/decisions/`, `docs/lessons.md`, `docs/standards/*`, `adapters/AGENTS.md`	The apply job rechecks item and admission state, validates Results, Effects, Findings, and Dispositions, and refuses invalid or superseded Results before writing. It records outcomes and Finding records from confirmed read-back, revokes minted tokens, and stops later writes after token refusal. Related tests and documentation describe the apply rules and implementation boundaries.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant Apply as harness/apply.py
  participant Identity as adapters/identity.py
  participant Effects as adapters/effects.py
  participant GitHub
  Apply->>Identity: mint repository-scoped token
  Identity-->>Apply: token with requested permissions
  Apply->>Effects: send permitted Role Effect
  Effects->>GitHub: submit or recover write
  GitHub-->>Effects: write response and read-back
  Effects-->>Apply: verified Effect state and surfaces
  Apply->>Apply: record confirmed Effects and Findings
  Apply->>Identity: revoke token

Possibly related issues

Issue 194: The change implements apply-time validation, Role Effects, narrowed credentials, read-back claims, and applied records described by the issue.
Issue 139: The apply job validates permitted Effects and refuses invalid ones, including Effects that do not meet the defined constraints.
Issue 185: The effects adapter adds item-scoped review-thread resolution with recovery and read-back verification.
Issue 250: The effects adapter adds review and check-run writes with identity, item, commit, and read-back checks.
Issue 306: The apply job records Role Effects from GitHub read-back, which provides the records the issue’s reconciliation must match.

Merge Risk: 🟡 Moderate · up to 57e15

The repository verification check fails on a decision-numbering gap. The apply job also compares run IDs without normalizing their type, which could wrongly refuse a Run once the workflow is wired. Resolve both before merging.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 38.61% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 101 functions across 5 files. (34 skipped…	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks: 4 passed

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly identifies the three main changes: apply refusals, the identity port, and Role writes. The issue and PR references add minor noise but do not make the title unclear.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

Docstring coverage is 38.61% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 101 functions across 5 files. (34 skipped: 34 unsupported.)

Resolution

Write docstrings for the functions missing them to satisfy the coverage threshold.

✨ Finishing Touches: 💡 2

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⚔️ Resolve merge conflicts: 💡

Resolve merge conflict in branch harness/apply

🧪 Generate unit tests (beta)

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chatgpt-codex-connector · 2026-10-22T18:03:15Z

Codex Review Summary

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

Review	Status	Commit	Review trigger
📝 Code Review	⚠️ Failed 2026-10-22T19:52:12.743628Z We couldn’t complete this review. Comment `@codex review` to try again.	`2eff739`	New commits

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…eeds READS names The Maintainer expands combsmith-sf-pr-review rather than giving factory-apply a second key (2026-10-22): checks write, actions read and issues read. identity.granted narrows any needs as permissions narrows an Effect's, and harness/apply.py's READS names every fact the Kernel is asked on and the run records. The App's grants wait on the registration and P-39 run again, so the test of the live grant is pending; record 0054 says so, and leaves #196 only the wiring. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…ecurity pass and Argon - A comment on the item is recovered by its place among the Run's comments on the item alone. None is sent after one on the item that was not written, so a retry neither posts twice nor claims another comment. - A resolved thread is an accepted Disposition. Only the owner of the thread's category resolves it, and only on its own decision, in the same Result, to accept it. - A count of active Runs that cannot be this Run's, a flag or one under it, is left as read, so the Kernel defers on it (Argon's blocker). - A token GitHub made other than asked is revoked before the refusal. No answer, or a repository list that is not one, is refused and never escapes the mint. - role_permits pins a check run's name and commit, and a resolution to the item's own threads. - A check run is claimed only read back completed, under its name, with its conclusion. A review's threads are claimed only when the count agrees and each comment has a number. A review comment's surface must be a thread, and an annotation's must be this check run's key and its ref. - A comment's start is its Run's record's, or, while the Run is unnamed, its run's creation. Each fix has its test, and the guards the reviews found unheld have theirs. 26 mutants added, 8 re-pointed and 2 made equivalent removed. All 141 of the PR's mutants are hand-checked killed the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

…into harness/apply # Conflicts: # adapters/AGENTS.md # harness/AGENTS.md # tools/mutants.py

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🪄 Fix comments: Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at
@docs/decisions/0054-apply-writes-a-roles-effects-with-a-token-narrowed-to-them-and-claims-only-what-it-reads-back.md:
- Line 1: Update decision record 0054 and the decision sequence so numbering is
contiguous from 0001 with one decision per file; add the missing 0053 record or
renumber this record and update its references to eliminate the gap.

Review comments at @harness/apply.py:
- Around line 96-98: Normalize the run ID to a string in apply’s
unidentified_runs filtering and since lookup before comparing it with each
record’s run ID; preserve no-match behavior when the run ID is absent. Update
the related tests to use string run IDs.

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ℹ️ Review info

⚙️ Run configuration

Source mode: Auto
Repository: combsmith/software-factory
Branch: main
File: .coderabbit.yaml
Commit: 91fb60b
Layers: Repository YAML
Review profile: CHILL
Plan: Advanced
Run ID: b598b5d8-e29d-4fb6-adb3-0cf505c472e1

📥 Commits

Reviewing files that changed from the base of the PR and between 91fb60b and 57e1554.

📒 Files selected for processing: 39

adapters/AGENTS.md
adapters/effects.py
adapters/identity.py
config/apps.json
docs/architecture/software-factory-design.md
docs/decisions/0004-one-run-contract-and-a-job-is-a-credential-boundary.md
docs/decisions/0005-each-role-writes-through-its-own-app.md
docs/decisions/0007-an-approval-is-bound-to-content.md
docs/decisions/0012-lenses-report-findings-and-the-kernel-decides-convergence.md
docs/decisions/0015-a-lens-is-read-from-its-own-app-and-only-what-gates-holds-a-merge.md
docs/decisions/0018-a-lens-is-read-from-its-own-app-and-workflow-and-only-what-gates-holds-a-merge.md
docs/decisions/0020-a-change-to-the-factorys-own-rules-or-a-lenss-inputs-is-reviewed-by-a-model-lens.md
docs/decisions/0022-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md
docs/decisions/0025-acceptance-is-read-from-its-reporter-against-the-contract-a-person-approved.md
docs/decisions/0026-a-lens-is-read-from-its-own-app-and-workflow-its-job-judges-every-job-it-waits-on-and-only-what-gates-holds-a-merge.md
docs/decisions/0029-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported.md
docs/decisions/0036-a-run-listed-before-its-name-is-unidentified-and-defers-every-admission.md
docs/decisions/0038-a-result-asks-and-names-no-one-and-apply-writes-the-finding-it-posted.md
docs/decisions/0039-one-envelope-on-what-crosses-a-boundary-whole.md
docs/decisions/0049-a-reviewing-run-that-leaves-a-criterion-uncovered-has-not-reported-and-one-that-ran-and-left-no-outcome-is-an-attempt.md
docs/decisions/0050-the-model-is-given-a-task-and-no-tool-and-apply-writes-only-what-it-reads-back.md
docs/decisions/0054-apply-writes-a-roles-effects-with-a-token-narrowed-to-them-and-claims-only-what-it-reads-back.md
docs/lessons.md
docs/standards/security-boundaries.md
examples/invalid/apps.a-key-in-an-environment-no-job-holds.json
examples/invalid/apps.a-name-without-the-prefix.json
examples/invalid/apps.a-need-not-in-the-table.json
examples/invalid/apps.a-need-the-table-leaves-out.json
examples/invalid/apps.a-permission-github-does-not-have.json
examples/invalid/apps.a-permission-with-no-need.json
examples/invalid/apps.a-repo-not-named-for-slice-0.json
examples/invalid/apps.admin-is-not-a-level.json
examples/invalid/apps.installed-across-the-org.json
harness/AGENTS.md
harness/apply.py
schemas/apps.schema.json
tests/AGENTS.md
tests/test_apply.py
tools/mutants.py

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- A token GitHub does not confirm revoked ends the Run environment, token_not_revoked; the Effects stay recorded. - A 401 or 403 on any request of a Role write, a recovery read or a read-back among them, ends that write refused, token_refused, so no later write is sent on the credential. _fault's refused branch can no longer be reached, and goes. - A Result with two reviews is refused, review_twice: a review is recovered as this App's one on this commit. - A comment is recovered only from this App's comments created since the Run began, since GitHub lists those updated since then. - A posted Finding with no start line is refused, finding_has_no_place, never placed on line 1. - An unidentified Run's id and this job's GITHUB_RUN_ID are compared as text, as the records port gives the id. 7 mutants added, 5 re-pointed and 2 made equivalent removed; all of the PR's mutants are hand-checked killed the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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- A security thread is resolved by no Role: its owner may accept only on the author's proposal of fixed or not applicable, which is in another Run's Result that apply cannot read yet (security_proposal_unread). It waits on the fix Intent. Record 0054 says so. - A grant of no level, or an App with no grants, is refused, not a crash. - role_permits holds a review's commit to the item's head, and a check run's conclusion to success and its external_id to the Run's and the Effect's. - A comment on the item whose Run's start was not read mints nothing and writes nothing (run_start_unread). Muse's other findings were fixed in the rounds before: two reviews in one Result, a comment's place, and a check run's read-back. 7 mutants added, 1 re-pointed, each hand-checked killed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Codex's second round put the commit pin on the line this mutant changes, so CI's shard 1 read it as stale. It is re-pointed and hand-checked killed; every mutant's text is found once. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

chatgpt-codex-connector · 2026-10-22T19:14:47Z

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Codex's pins on a check run's conclusion and key refused the allowlist test's bad check runs whatever else was wrong, so the mutants on its name, commit and status lived in CI. Each bad case is now the good body with one key changed, beside the good body, which passes. All 153 of the PR's mutants are hand-checked killed the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

chatgpt-codex-connector · 2026-10-22T19:24:08Z

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- A Finding whose range ends before it starts is refused, finding_has_no_place, before anything is minted or written. - A check run is recovered from every run of its name on the commit (filter=all), so a later run never hides an earlier one with this Effect's external_id; role_permits allows only that form. A comment on a deleted line keeps side RIGHT: a Result's location names the head's lines. 2 mutants added and 2 re-pointed; all 155 of the PR's mutants are hand-checked killed the CI way. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

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sonarqubecloud · 2026-10-22T19:53:17Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

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

See analysis details on SonarQube Cloud

…pproval, and 0054 closes the gap The effects port keeps both: #319's Role writes and the approval. The approval takes #319's _body, which is the same; it keeps its own reader, _asked, since #319's _sent ends the Role's writes on a refused token by raising, where the approval classes a refused token by its status (ruling 6). harness/AGENTS.md names both and stays within 40 lines. One mutant reads text now unique to the approval. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

don-petry and others added 30 commits October 21, 2026 19:01

Merge remote-tracking branch 'origin/main' into harness/run-task

40bb97a

# Conflicts: # config/hooks.json # tools/mutants.py

Harness: one description for harness/ on the list (#194, PR 1)

e851996

harness/ is verify's input and, since #140, pr-review's own. The stop lists a path once, by its first entry, so both entries carry the same description. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Harness: #194's record takes 0050, by the orchestrator's order (#194,…

25e2357

… PR 1) #298 takes 0048 and #302 takes 0049, so this record is 0050; #304 enqueues once #302 has merged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/main' into harness/run-task

eb01f1e

Effects port: its record is decision 0051, numbered at enqueue after #…

7fefb6d

…298 (0048), #302 (0049) and #304 (0050) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Merge branch 'main' of https://github.com/combsmith/software-factory …

6b47640

…into harness/run-task # Conflicts: # docs/decisions/0020-a-change-to-the-factorys-own-rules-or-a-lenss-inputs-is-reviewed-by-a-model-lens.md

Merge remote-tracking branch 'origin/main' into harness/run-task

de909a1

Record 0049: its apply row waits on harness/apply.py, now that harnes…

46f5c5d

…s/ exists Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Harness and adapters pages fit their limits; the test token and impor…

eb7b4ce

…ts pass check_repo Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Merge main into controller/effects

3611af1

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Identity test: an unreadable key in no key's shape, so the secret sca…

e8b2463

…n finds none Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/controller/effects' into harness…

764f333

…/apply # Conflicts: # adapters/AGENTS.md # tools/mutants.py

Merge remote-tracking branch 'origin/main' into harness/apply

20a347f

# Conflicts: # adapters/AGENTS.md # adapters/effects.py # tests/test_effects.py # tools/mutants.py

Merge remote-tracking branch 'origin/main' into harness/apply

7ba8594

don-petry and others added 2 commits October 22, 2026 12:47

apps/1 names the check run's need, and record 0054 names the push as …

5e68e93

…a wait Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

apps/1's examples name the check run's need, waiting

d307784

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

don-petry requested a review from a team as a code owner October 22, 2026 18:03

don-petry and others added 3 commits October 22, 2026 13:04

Merge branch 'main' of https://github.com/combsmith/software-factory …

ef5b0b7

…into harness/apply # Conflicts: # adapters/AGENTS.md # harness/AGENTS.md # tools/mutants.py

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Comment thread ...y-writes-a-roles-effects-with-a-token-narrowed-to-them-and-claims-only-what-it-reads-back.md

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don-petry mentioned this pull request Oct 22, 2026

Harness: the approving act, the machine user's approval of the commit it read, through its own token alone (#195, PR 1) #321

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don-petry added this pull request to the merge queue Oct 22, 2026

Merged via the queue into main with commit 70f690a Oct 22, 2026
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don-petry deleted the harness/apply branch October 22, 2026 20:28

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