fix: make package quality gates honest

.llm/runs/release-0.0.7-internals--orchestration/slices/package-gate-honesty/codex-thread-ids.md

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+# package-gate — Codex implementation thread
+- **Thread / session id:** `01a004ec-86a6-7c21-8886-81c09de099f5`
+- **Rollout:** `/home/codex/.codex/sessions/2026/08/15/rollout-2026-08-15T12-16-45-01a004ec-86a6-7c21-8886-81c09de099f5.jsonl`
+- **Worktree:** `/home/codex/repos/netscript-007-package-gate`
+- **Branch:** `fix/package-gate-honesty` @ `05fc3132b` (NO upstream by design).
+- **Push rule:** explicit refspec only — `git push origin HEAD:refs/heads/fix/package-gate-honesty`.
+- **Requested route:** provider=openai · model=gpt-5.6-sol · effort=medium
+- **Observed route:** provider=openai · model=gpt-5.6-sol · effort=medium
+- **Route verdict:** matched
+- **Runtime:** approval=never · sandbox=dangerFullAccess
+- **Brief (staged):** `/home/codex/package-gate-brief.md`
+## Steering (same thread — never a second send-message-v2 at this worktree)
+```bash
+codex exec resume 01a004ec-86a6-7c21-8886-81c09de099f5 -- "<follow-up>"
+```
+_Written by `.llm/tools/agentic/codex/launch-codex-slice.ts`._

.llm/runs/release-0.0.7-internals--orchestration/slices/package-gate-honesty/context-pack.md

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+# Context Pack: package-gate-honesty
+
+## Run Metadata
+
+| Field          | Value                                                                 |
+| -------------- | --------------------------------------------------------------------- |
+| Run ID         | `release-0.0.7-internals--orchestration/slices/package-gate-honesty`  |
+| Branch         | `fix/package-gate-honesty`                                            |
+| Current phase  | cycle 2 `FAIL_PLAN`; thirteen-path repair pending Tier-A owner review |
+| Archetype      | `6 — CLI / Tooling` (supporting MCP member A2)                        |
+| Scope overlays | `docs`                                                                |
+
+## Current state
+
+PLAN-EVAL cycle 1 correctly returned `FAIL_PLAN` at evaluator commit `be2b18728`: root exclusion
+cannot affect the optimized wrappers' explicit argv. The coordinator granted child-only marker
+semantics plus nearest-config batching in both wrappers, then granted the exact formatting-only
+twelfth path exposed by the honest 114-file finding. Both exact no-extra-flag prototypes are now
+green at 114; all four healthy files remain selected, parsed meaning is equal, doctor is 4/4, and
+the malformed hash is unchanged. Cycle 2 correctly returned `FAIL_PLAN` at evaluator commit
+`c415daad2`: the lint wrapper is embedded in published CLI source. The coordinator granted the exact
+generated barrel as path thirteen and ruled on root task selection, fixture-style wording, and
+nearest-config memoization. No checkout product/config/generated implementation exists.
+
+## Completed
+
+- Bootstrap commit `25c29575c` pushed with explicit refspec.
+- Draft PR #1663 opened with exact closing keywords, checkable DoD, `type:fix`, `area:tooling`,
+  `status:research`, milestone `0.0.7`; no acceptance-evidence blocks.
+- All three issues re-read live.
+- Three cwd failures and MCP fmt config crash reproduced through structured wrappers.
+- `closeScoreGap` definition, consumption, and decorative test behavior traced.
+- Thirteen-path repaired plan and per-member JSR audit plan locked; no fourteenth path.
+- Exact no-extra-flag lint prototype green at 114; fmt reports exactly one genuine healthy-fixture
+  finding at 114; separate fmt/lint negative controls red with real findings; doctor 4/4; all
+  negative-control source files restored byte-exactly.
+- Scratch-only formatting of the granted twelfth path makes exact fmt green at 114 while lint and
+  doctor remain green; original/formatted exports are equal.
+- All four healthy TS files were individually named selected by genuine or controlled fmt findings,
+  and every controlled probe was restored byte-exactly.
+- Cycle-2 archive proof established that canonical lint-wrapper regeneration changes only
+  `agent-tools.generated.ts` among generated assets, including its embedded tool text and bundle
+  hash; `check:assets-barrel` is now planned.
+
+## In progress
+
+- Awaiting Tier-A/owner review after the second and final ordinary `FAIL_PLAN` cycle.
+
+## Next steps
+
+1. Topic supervisor reviews the repaired thirteen-path plan under owner escalation.
+2. No cycle 3 is requested or assumed; implementation authority exists only after the supervisor
+   explicitly disposes the exhausted plan gate.
+3. If authorized later, implementation follows S1-S4; `scaffold.runtime` remains waived `n/a` and
+   must not run.
+
+## Key decisions
+
+| Decision                                     | Source         | Notes                                                          |
+| -------------------------------------------- | -------------- | -------------------------------------------------------------- |
+| Child marker + config batching owns boundary | plan L3/L4     | Both green at 114 after granted formatting-only normalization. |
+| Published lint asset regenerated canonically | plan L7/S1     | Embedded tool text/hash change; no export/API-shape change.    |
+| Root task parent skip removed                | plan S1/gates  | Top-level raw-walk exclusion retained for fixture-local style. |
+| Module-derived CLI paths                     | plan L1/L2     | No ambient cwd and no weakened assertion.                      |
+| `0.5` pinned both directions                 | plan L5/L6     | Inside/outside identity conflict makes movement observable.    |
+| Formal PLAN-EVAL required                    | plan judgement | This thread cannot self-launch or self-certify.                |
+
+## Authoritative product/config edit surface
+
+1. `deno.json`
+2. `packages/cli/e2e/src/application/gates/scaffold/service-env/service-env-gates_test.ts`
+3. `packages/cli/e2e/tests/presentation/quickstart-command-drift_test.ts`
+4. `packages/cli/e2e/src/application/gates/scaffold/run-documented-stream-example.ts`
+5. `packages/mcp/src/domain/docs/guidance-index.ts`
+6. `packages/mcp/tests/guidance-retrieval_test.ts`
+7. `.llm/tools/run-deno-fmt.ts`
+8. `.llm/tools/run-deno-fmt_test.ts`
+9. `.llm/tools/run-deno-lint.ts`
+10. `.llm/tools/run-deno-lint_test.ts`
+11. `packages/mcp/tests/fixtures/doctor/broken/.deno-fmt-lint-ignore`
+12. `packages/mcp/tests/fixtures/doctor/healthy/netscript.config.ts`
+13. `packages/cli/src/kernel/assets/agent-tools.generated.ts` (canonical regeneration only)
+
+Everything else in the frozen outer bound is read-only, especially both docs sources and the broken
+fixture config. A fourteenth path is rescope.
+
+## Gates
+
+| Gate family | Current status                        | Evidence                                       |
+| ----------- | ------------------------------------- | ---------------------------------------------- |
+| Plan-Gate   | cycle 2 `FAIL_PLAN`; owner escalation | `plan-eval.md`; repaired `plan.md`.            |
+| Static      | NOT_RUN                               | No implementation.                             |
+| Fitness/JSR | planned                               | `research.md` and `plan.md` per-member tables. |
+| Runtime     | N/A                                   | Explicit coordinator waiver; must not run.     |
+| Consumer    | baseline failures reproduced          | `worklog.md` research diagnostics.             |
+
+## Open questions
+
+- None that change implementation shape; implementation authority still depends on explicit
+  Tier-A/owner disposition. No cycle 3 is requested or assumed.
+
+## Drift and debt
+
+- Drift: R8 falsified by execution; rejected parent-family false exclusion; corrected 114-file
+  proof; authorized formatting-only twelfth path; cycle-2 published-asset discovery; authorized
+  generated thirteenth path; corrected root-vs-fixture formatting semantics.
+- Debt: no new/closed entry; named CLI/MCP baseline debt remains unchanged.
+
+## Commits
+
+- Draft PR commit list + phase comments are authoritative; no `commits.md`.

.llm/runs/release-0.0.7-internals--orchestration/slices/package-gate-honesty/drift.md

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+# Drift Log: package-gate-honesty
+
+Drift is append-only. Record facts that diverge from the plan, RFC, doctrine, or current-state
+documentation.
+
+## 2026-08-15 — Coordinator thread record preseeded the run directory
+
+- **What:** The first ground-truth status check found only
+  `.llm/runs/release-0.0.7-internals--orchestration/slices/package-gate-honesty/codex-thread-ids.md`
+  as untracked content.
+- **Source:** `git status --short` and the launcher-generated file contents.
+- **Expected:** A completely clean worktree before bootstrap.
+- **Actual:** The agentic launcher had staged this exact session's identity in the target run dir.
+- **Severity:** minor
+- **Action:** accept
+- **Evidence:** `codex-thread-ids.md` identifies this thread, worktree, branch, base, and matched
+  route.
+
+## 2026-08-15 — Root task exclusion does not satisfy standalone formatter acceptance
+
+- **What:** Root `fmt:check` already supplies a wrapper-level exclusion for the MCP doctor fixture,
+  but the exact standalone scoped command in #1618 still selects fixture TS and aborts during nested
+  config discovery.
+- **Source:** `deno.json:139-148`; exact wrapper reproduction in `worklog.md`.
+- **Expected:** The issue report could have implied no exclusion existed anywhere.
+- **Actual:** Task-level selection is protected, but the reusable standalone wrapper remains red.
+- **Severity:** minor
+- **Action:** fix
+- **Evidence:** Baseline 115 selected / one config crash; explicit wrapper exclusion 110 selected /
+  exit 0.
+
+## 2026-08-15 — R8 root-exclusion conclusion falsified by execution
+
+- **What:** Research R8 and plan L3 claimed root `deno.json` `exclude` would make the exact
+  optimized wrapper command green.
+- **Source:** Separate-session PLAN-EVAL cycle 1 at evaluator commit `be2b18728`; accepted
+  coordinator finding.
+- **Expected:** Root exclusion would prevent Deno from consuming the malformed fixture config.
+- **Actual:** Both wrappers select files independently and pass explicit argv. Deno resolves each
+  named file's nearest config, so root exclusion is not consulted by selection and the batch
+  crashes.
+- **Severity:** significant
+- **Action:** fix in plan; retain root exclusion only as non-load-bearing native directory-walk
+  protection.
+- **Evidence:** `plan-eval.md` §1; baseline fmt/lint matrix in `worklog.md`.
+
+## 2026-08-15 — Coordinator granted eleven-path marker rescope and runtime waiver
+
+- **What:** The authoritative implementation surface grew from six to eleven paths: both optimized
+  wrappers, both wrapper tests, and one narrowly named marker beside the malformed fixture were
+  added. The coordinator selected the marker family and waived `scaffold.runtime` as gate-matrix
+  `n/a`.
+- **Source:** Topic-supervisor resume instruction after PLAN-EVAL cycle 1.
+- **Expected:** Original plan prohibited `.llm/tools/**` and awaited a serialized runtime lease.
+- **Actual:** Wrapper changes are explicitly authorized; adding a twelfth path is still rescope. The
+  expensive gate must not run and is not `NOT_RUN` pending a lease.
+- **Severity:** significant (authorized rescope)
+- **Action:** accept and repair plan; no implementation before cycle-2 `PASS`.
+- **Evidence:** Eleven-path table and gate row 7 in repaired `plan.md`.
+
+## 2026-08-15 — Child-only marker interpretation remained red
+
+- **What:** A scratch prototype that skipped only `doctor/broken/` removed the malformed config's
+  single TS file but did not produce a truthful fmt verdict.
+- **Source:** `git archive HEAD` proof under `.llm/tmp/`; no checkout product/config edits.
+- **Expected:** Marker-local subtree skip might be sufficient at 114 selected files.
+- **Actual:** Deno next exposed the root/healthy nested-config conflict; after config-aware
+  batching, fmt still found the healthy fixture's root-style drift. The accepted explicit
+  parent-scope marker omits exactly the five-file doctor family and yields the established 110-file
+  surface.
+- **Severity:** significant design finding
+- **Action:** reject child-only semantics; lock the narrowly named `.deno-fmt-lint-ignore-parent`
+  convention and test both marked and unmarked directions.
+- **Evidence:** Executed pre-plan matrix and exact collateral list in `worklog.md`.
+
+## 2026-08-15 — Parent-family marker draft rejected before push
+
+- **What:** Local plan-repair commit `71e803807` proposed `.deno-fmt-lint-ignore-parent`, which made
+  both wrappers green by dropping the entire five-file `doctor/` family.
+- **Source:** Topic-supervisor correction received before any push; independent arithmetic and
+  archive proof.
+- **Expected:** The marker must skip only its own marked subtree while an unmarked sibling remains
+  selected.
+- **Actual:** The parent marker dropped `broken/netscript.config.ts` plus all four unmarked healthy
+  TS files (115→110), converting a loud real finding into a silent false-positive exclusion.
+- **Severity:** significant plan correction
+- **Action:** reject and amend before push. Lock child-only marker semantics plus nearest-config
+  batching; preserve all four healthy files in the 114-file selection.
+- **Evidence:** Corrected 114-file matrix in `worklog.md`; remote branch remained at `be2b18728`, so
+  the rejected commit was never published.
+
+## 2026-08-15 — Honest 114-file proof reveals one pending twelfth path
+
+- **What:** With child-only marker and nearest-config batching, lint is green but fmt reports one
+  genuine finding in unmarked `doctor/healthy/netscript.config.ts`.
+- **Source:** Corrected `git archive HEAD` proof; coordinator independently reproduced the
+  file-level finding.
+- **Expected:** Removing batch poisoning should expose real findings rather than suppress them.
+- **Actual:** Exactly one marked file leaves selection. The remaining healthy source has no
+  competing fmt configuration; it is simply unformatted. Formatting only that file in scratch makes
+  exact fmt green at 114 while lint and doctor remain green.
+- **Severity:** significant pending rescope
+- **Action:** prepare proof only; do not touch the checkout path until the coordinator grants it as
+  a twelfth path. Implementation and PLAN-EVAL cycle 2 remain blocked.
+- **Evidence:** Proposed one-file diff and fmt/lint/doctor results in `worklog.md`.
+
+## 2026-08-15 — Coordinator granted formatting-only twelfth path
+
+- **What:** The coordinator added `packages/mcp/tests/fixtures/doctor/healthy/netscript.config.ts`
+  to the planned implementation surface, bringing the bound to twelve paths.
+- **Source:** Topic-supervisor grant after review of plan head `ccf256884` and the honest R14/R15
+  scratch proof.
+- **Expected:** The real 114-file fmt finding must be fixed without hiding any unmarked file.
+- **Actual:** Deno formatting alone expands the object and normalizes quotes. Original and formatted
+  modules both export `{"plugins":["workers"]}`; both exact wrappers are green at 114, doctor is
+  4/4, and the malformed config hash remains
+  `6815999dbd68bd1ab5bb137b59808cb1f1a38fb3393c9133721f439c0ad37361`.
+- **Severity:** significant authorized rescope
+- **Action:** accept in the plan only. Do not mutate the checkout path before fresh Tier-A and
+  PLAN-EVAL cycle 2 `PASS`; no thirteenth path exists.
+- **Evidence:** Final green matrix, four individually named healthy selection probes, semantic
+  equality, and byte-restoration evidence in `worklog.md`.
+
+## 2026-08-15 — Cycle-2 evaluation exposed a published consumer asset
+
+- **What:** The twelve-path plan treated `.llm/tools/run-deno-lint.ts` as maintainer-only, but the
+  canonical CLI asset generator embeds it verbatim in published
+  `packages/cli/src/kernel/assets/agent-tools.generated.ts`.
+- **Source:** Separate-session PLAN-EVAL cycle 2 at evaluator commit `c415daad2`, independently
+  confirmed by the coordinator.
+- **Expected:** The plan claimed no CLI publish delta and omitted generated-asset freshness.
+- **Actual:** The planned lint-wrapper edit changes installed consumer behavior, embedded tool text,
+  and `EMBEDDED_AGENT_TOOL_BUNDLE_HASH`; `check:assets-barrel` would fail unless the generated
+  barrel changes too.
+- **Severity:** significant plan correction
+- **Action:** accept coordinator grant of exactly the generated barrel as path thirteen;
+  regeneration must use `deno task gen:assets-barrel`, never a hand edit. Add the freshness gate and
+  disclose the consumer/JSR delta. No fourteenth path exists.
+- **Evidence:** Full archive-copy generator proof in `plan-eval.md` §7; research R16 and repaired
+  plan L7/S1/JSR/gate rows.
+
+## 2026-08-15 — Fixture-format explanation and root exclusions corrected
+
+- **What:** The earlier drift entry called `healthy/netscript.config.ts` "simply unformatted" and
+  treated root exclusion as only non-load-bearing protection. The root task also retained a
+  wrapper-level parent-family skip.
+- **Source:** PLAN-EVAL cycle 2 advisories A1/A2 and the coordinator's binding rulings.
+- **Expected:** The honest gate should apply the fixture's own config without allowing either a raw
+  root walk or a task-level selection filter to undo coverage.
+- **Actual:** The original bytes are valid under root style (`singleQuote: true`, width 100) but
+  invalid under the authoritative fixture-local config's defaults (double quotes, width 80). The
+  top-level root `exclude` is load-bearing for raw formatter walks because it prevents reversion to
+  root style, while it remains non-load-bearing for the standalone explicit-argv acceptance command.
+  Conversely, the `fmt:check` task's wrapper `--exclude` silently drops the whole doctor family and
+  must be removed.
+- **Severity:** significant plan clarification
+- **Action:** preserve the historical wording above as append-only drift, supersede it here, update
+  R14/L3/L10/worklog, retain only the top-level raw-walk boundary, and plan memoized `nearestConfig`
+  resolution per directory before root-scale execution.
+- **Evidence:** `plan-eval.md` §2/§5 and advisories A1/A2/A4; repaired `plan.md` L3/L10/L11 and gate
+  row 3.
+
+## 2026-08-15 — Ordinary PLAN-EVAL allowance exhausted; owner escalation owns disposition
+
+- **What:** Cycle 2 returned `FAIL_PLAN`; the harness allows only two `FAIL_PLAN` cycles before
+  escalation.
+- **Source:** `plan-eval.md` at `c415daad2`; coordinator repair brief.
+- **Expected:** No implementation begins without a disposed plan gate.
+- **Actual:** The coordinator resolved every finding and granted the exact thirteenth path, but no
+  cycle 3 exists absent owner escalation.
+- **Severity:** process gate
+- **Action:** repair and publish run artifacts only, then stop for Tier-A/owner review. Do not
+  request or assume another evaluator run and do not implement.
+- **Evidence:** Repaired thirteen-path plan and this commit's worklog/context pack.