@lannguyensi/harness 0.38.0 → 0.39.0

package/CHANGELOG.md

@@ -5,6 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/),
 and this project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.39.0] - 2026-07-02
+
+**Headline: the 2026-07-01 deep-review remediation ships — enforcement no longer degrades under load, the `grounding:` section finally does something, and `apply --merge` stops eating operator edits.** The PreToolUse gate pools one grounding-mcp session per intercept (a hook timeout no longer silently fail-opens enforcement), `grounding.evidence_ledger.path` now actually configures the grounding-mcp entry, `apply --merge` preserves operator-added mcpServers with provenance, the Codex understanding-gate reaches approval-lifecycle parity with Claude Code, `diff --since` stops reporting override layers as phantom history, and CI gains two architecture fitness gates plus new `validate` lints (git-ignored OW knob, block policies without declared producers). Re-run `npm i -g @lannguyensi/harness` to upgrade.
+
+### Added
+
+- **Two architecture fitness functions now run in CI** (task 19e293c6, harness-review-2026-07-01). `npm run check:boundaries` (dependency-cruiser 18.0.0, `.dependency-cruiser.cjs`) pins the layering schema → policies → runtime → policy-packs → cli and fails on any new reverse import; running it for the first time surfaced four pre-existing shared-util edges (`policies/duration`, `policies/extract`, `runtime/ledger-record`, `runtime/expand-home` imported from below), which are grandfathered per target file and documented in the config with a pointer to the structural-concentration follow-up (f86b2425). `npm run check:duplication` (jscpd 5.0.11 via `scripts/check-duplication.mjs`) pins the clone count in `src/` at the post-extraction baseline of 82: a percentage threshold cannot see a single new ~16-line copy, an absolute count can — raising the pin requires an in-PR justification. Negative-control verified: a deliberate reverse import fails `check:boundaries` (exit 1), and the pre-extraction tree (85 clones) fails `check:duplication`.
+- **The `grounding:` manifest section is wired: `grounding.evidence_ledger.path` now configures the grounding-mcp entry** (task 129e1b94, harness-review-2026-07-01). `apply` projects the path as the `EVIDENCE_LEDGER_DB` env on the enabled grounding-mcp entry (the exact variable its ledger-bridge reads), `~`-expanded to an absolute path; an operator-declared env override wins. `adopt` mirrors the same synthesis so the apply→adopt round-trip stays drift-free, and `doctor` gains a Grounding section that checks the EFFECTIVE ledger path for writability and warns when an override diverges from the manifest value. `session.*`, `retention_days`, and `policies_source` stay RESERVED with explicit status comments (no consumer exists yet).
+- **Trust-model tripwire for custom `block` policies, plus a `validate` warning on undeclared producers** (task 43b107f2, harness-review-2026-07-01). writing-custom-policies.md gains a fourth "Read this first" tripwire spelling out that whoever can write the ledger can open a `requires:`/`ledger_tag` gate: block policies are advisory against the very agent they gate, and an enforcing gate needs a non-agent evidence actor. New `checkPolicySelfAttestation` in `validate` warns when a `block` policy declares no `producers:` at all (`require_approval` excluded with a recorded rationale); the recipes and templates now model the pattern, closing the agent-writable `risk-override` gap on the FULL_TEMPLATE's `gate-prod-destructive`. Engine hardening is tracked as follow-up task 078ec604.
+- **`harness validate` / `harness doctor` now warn when the solution-acceptance pack is enabled but the OW knob path is git-ignored** (task 24f6ceb9, ow-review-2026-07-01). The orchestrator-workflow arm reads repo state (`.ai/solution-acceptance.json` plus run completeness under `.ai/runs/`); a repo that ignores `.ai/` wholesale cannot commit its enforcement posture, so fresh clones and git worktrees silently skip the OW arm under the default `auto` knob. The shared check (`checkSolutionAcceptanceKnobIgnored`) probes `git check-ignore` against the process cwd, stays silent outside a git repository and in `doctor --shallow` runs (no spawns), and lands in the same Policy Packs section as the producer deadlock checks. Negative control: a repo that ignores only `.ai/runs/` produces no warning.
+
+### Changed
+
+- **`parseConfigUx` exists once** (task 19e293c6). The four byte-identical copies in hook-pre-tool-use, hook-codex-pre-tool-use, hook-branch-protection, and hook-solution-acceptance (the CHANGELOG had flagged the third copy for extraction; the fourth landed anyway because no scan existed) are now one shared helper in `src/cli/pack/hook-bootstrap.ts`, parameterized by the hook's stderr label. The per-hook warning output is byte-identical to the pre-extraction strings, pinned by a test per label.
+- **The harness repo itself now commits its OW enforcement posture** (task 24f6ceb9; operator-approved revision of the earlier ".ai/ fully gitignored" decision, which was about run noise). `.gitignore` narrows `.ai/` to `.ai/runs/`; `.ai/workflow/` (kit templates + manifest) and `.ai/solution-acceptance.json` (committed as `"orchestratorWorkflow": "on"`) are now tracked, so the solution-acceptance OW arm enforces in every checkout, including fresh clones and worktrees. `docs/policy-packs/solution-acceptance.md` gains a "Repo state and gitignore" section documenting the convention and the honest residual (run-to-change binding is agent-grounding `067bede3`).
+- **The symlink-rejecting gate-marker read exists once** (task f86b2425 slice 1). `checkApprovalMarker` (understanding-before-execution) and `readVerdict` (solution-acceptance) now share `readRegularFileRejectingSymlink` in `src/io/` (5-kind result; every deny detail and the exists-but-unreadable-still-satisfies semantic byte-identical). Future defensive fixes (lstat/read race, ENOTDIR handling) have a single home.
+
+### Fixed
+
+- **First run on a fresh machine no longer dead-ends** (task 24ec07a6, harness-review-2026-07-01). Every read verb (`doctor`, `describe`, `validate`, `list`, `explain`, ...) previously failed with a bare `manifest not found: <path>` when no `harness.yaml` exists; the base-manifest miss now appends `No harness.yaml on this machine yet: run harness init --interactive (or harness init --template solo) to create one` (same message shape, same exit 66; a missing override LAYER keeps the old message, since "run init" would be wrong advice for a mid-read race). Also fixed two doc-drift items the same review flagged: docs/for-agents.md's `${REPO}` row claimed "basename of cwd" (the code resolves the basename of the git worktree ROOT) and its `${BRANCH}` row promised a `(detached)` placeholder that has never existed (detached HEAD substitutes the empty string); docs/init-interactive.md's Custom-flow pack list was missing `branch-protection` and now notes that `solution-acceptance` is deliberately not wizard-selectable.
+- **A manifest with the wrong `version` now gets upgrade guidance instead of a bare zod literal error** (task 50a94127, harness-review-2026-07-01). `version: 2` produces `this CLI supports manifest version 1; your manifest declares version 2. A newer manifest needs a newer CLI: re-run npm i -g @lannguyensi/harness ...` on every parseManifest surface (`validate`, `doctor`, `describe`, ...); a manifest missing the key gets the distinct `missing manifest version: add version: 1` variant instead of wrong upgrade advice. Message wording only: issue codes, paths, error type, and exit codes are unchanged. Also corrected two dishonest schema comments: `risk:` was still annotated "no runtime surface reads them yet" in schema/index.ts and risk.ts although `risk.classifiers[]` has been live since Phase 7 (classifyRisk on every PreToolUse + `when.risk.*` in when-eval); and the genuinely inert keys `memory.scopes` / `memory.retention.broken_refs` now carry explicit `STATUS: INERT` disclosure comments (validated, read by no consumer) instead of looking like live configuration.
+- **`apply --merge` no longer clobbers operator-added `mcpServers` entries — and manifest-removed/disabled servers still leave the target** (task 059b669c, harness-review-2026-07-01; operator decision: deep-merge over warn-only). The merge is now per server name inside `mcpServers`, with provenance from `.last-apply`: names the manifest declares come from the generated output; a server the operator hand-added directly to the target settings.json survives (`kept N operator-added mcpServer(s) (...)` in the apply summary); a server harness wrote on a previous apply that the current manifest no longer emits (deleted, or `enabled: false`) is dropped (`dropped N manifest-removed mcpServer(s) (...)`), so `enabled: false` remains an effective kill switch on `--merge` targets. Without provenance (no `.last-apply` yet, a record without a settings.json entry, or a corrupt record) unknown names are conservatively preserved. `hooks` stays wholesale-owned (no stable per-entry identity in the settings shape; hand-added hooks belong in the manifest via `harness adopt`). The merge remains idempotent, and a malformed (non-object) `mcpServers` on either side falls back to the old wholesale replace.
+- **`adopt` no longer drops hook `timeout` or MCP `min_version`/`version_command` on the round-trip** (task 059b669c). `parseSettingsHooks` now captures a settings hook's `timeout` (positive integers only) and `buildHookEntry` carries it into `budget_ms` — 1:1 with apply's projection, so adopt→apply round-trips the value losslessly for newly adopted hooks (a timeout-only hand-edit to an already-declared hook is deliberately ignored: `timeout` is not part of the drift key, because hooks adopt add-only and a timeout-only difference would otherwise create a duplicate entry — pinned by a test). `buildMcpEntry` now also carries forward `min_version`/`version_command` from the existing manifest entry on a replace-modified drift (previously only `health` and `enabled: false`, despite the comment claiming full manifest-only-field preservation; the comment now enumerates exactly what is carried).
+- **The Codex understanding-gate PreToolUse hook now honors `approval_lifecycle` and task-scoped markers** (task e7c2ec3c, harness-review-2026-07-01). The Codex hook previously called the bare session-marker check, so `approval_lifecycle.max_age` (expired approvals) and the active-claim task-scoped marker silently applied only to Claude Code sessions — a stale Codex approval still opened the gate, and a task-scoped `harness approve understanding --task` marker was invisible to Codex. Both hooks now resolve markers through one shared code path (`checkOperatorApprovalMarkers` in the understanding-before-execution runtime): task-scoped marker first, session marker second, both under the same TTL. The Claude hook's stderr/decision contract is unchanged; the Codex hook gains the same task-scope trace line on a miss. Pinned by five parity tests (expired blocks / fresh allows / task-scoped allows / different-task marker blocks / stale task marker blocks). Known residual: the pack wires no Codex PostToolUse hook, so `expire_on_tool_match` boundaries still do not fire in Codex sessions (tracked as a follow-up task).
+- **The PreToolUse runtime gate no longer spawns two grounding-mcp subprocesses per matching policy** (task a2589fa3, harness-review-2026-07-01). `harness policy intercept` previously spawned them sequentially per policy; under load that approached the 30s hook budget, and a hook timeout is conventionally fail-open, so enforcement silently stopped exactly when contention was highest. One lazily-spawned grounding-mcp session per intercept invocation now multiplexes `ledger_summary`/`ledger_add` over a single stdio pipe, with a per-session summary cache (the K per-policy queries are identical and collapse into one) and a session-level timeout latch bounding worst-case ledger time at ~1 timeout. Decision semantics untouched: serial evaluation, first blocking decision in manifest order owns the deny envelope, warn-degraded never blocks.
+- **`harness diff --since <ref>` no longer reports the override merge itself as phantom diffs** (task b2660f9e, harness-review-2026-07-01). The ref side previously compared a bare `git show <ref>:harness.yaml` against the override-merged present, so any operator using override layers saw the merge as diffs indistinguishable from real manifest history. The ref side now merges the SAME resolved layers: a versioned layer is read at the ref (true layer history), a layer added since the ref is a real effective-config change, and a non-versioned layer (e.g. a `~/.harness` home elsewhere) is applied to both sides so the constant cancels out — surfaced via `DiffResult.warnings` on stderr, keeping stdout a pipeable diff.
+
 ## [0.38.0] - 2026-06-27
 
 **Headline: the Risk Gate now flags fail-closed unclassified matches across the audit trail, and `validate` / `doctor` lint risk policies that forgot to scope by `environment.name`.** When a risk-gate policy fires only because the action was unclassified (the "unknown is not safe" rule), `harness audit` (table and `--json`) and `harness explain --trace` now mark the decision, so an operator reviewing a deny can tell a real critical-severity match from a fail-closed one. A new lint, shared by `harness validate` and `harness doctor`, warns when a `when:` block gates on `risk.severity_at_least` / `risk.category_in` / `action.reversible` without an `environment.name` scope (those clauses match every unclassified command in every environment). Re-run `npm i -g @lannguyensi/harness` to upgrade.

package/dist/cli/add/index.js

@@ -44,7 +44,12 @@ export async function add(action, opts = {}) {
     // We use parseManifest (not the result of validateBeforeWrite) so we have a
     // typed Manifest for runAssetChecks. defaults flow through.
     const manifest = parseManifest(parseYaml(proposed));
-    const proposedErrors = runAssetChecks(manifest, { homeDir: opts.homeDir }).filter((d) => d.severity === "error");
+    // gitIgnoreProbe stays null: the knob-ignored check is warning-only and
+    // this gate consumes errors, so the git spawn would be wasted work.
+    const proposedErrors = runAssetChecks(manifest, {
+        homeDir: opts.homeDir,
+        gitIgnoreProbe: () => null,
+    }).filter((d) => d.severity === "error");
     // Compute a baseline error set from the original manifest so that
     // pre-existing asset problems unrelated to this add do not block it.
     // If the original manifest cannot be parsed (broken base), fall back to
@@ -52,7 +57,10 @@ export async function add(action, opts = {}) {
     let baselineKeys = new Set();
     try {
         const baselineManifest = parseManifest(parseYaml(original));
-        const baselineErrors = runAssetChecks(baselineManifest, { homeDir: opts.homeDir }).filter((d) => d.severity === "error");
+        const baselineErrors = runAssetChecks(baselineManifest, {
+            homeDir: opts.homeDir,
+            gitIgnoreProbe: () => null,
+        }).filter((d) => d.severity === "error");
         baselineKeys = new Set(baselineErrors.map((d) => `${d.severity}|${d.path}|${d.message}`));
     }
     catch {

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cli/add/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,KAAK,IAAI,SAAS,EAAE,MAAM,MAAM,CAAC;AAC1C,OAAO,EAAE,eAAe,EAAE,MAAM,0BAA0B,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAChD,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAChD,OAAO,EACL,sBAAsB,EACtB,mBAAmB,GACpB,MAAM,mCAAmC,CAAC;AAC3C,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AACtD,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACzE,OAAO,EAAE,QAAQ,EAAiB,MAAM,aAAa,CAAC;AAiBtD,MAAM,gBAAgB,GAAG,cAAc,CAAC;AACxC,MAAM,aAAa,GAAG,eAAe,CAAC;AAEtC,SAAS,iBAAiB,CAAC,IAAgB;IACzC,IAAI,IAAI,CAAC,UAAU;QAAE,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IAC1D,OAAO,IAAI,CAAC,IAAI,CACd,cAAc,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,IAAI,EACzF,gBAAgB,CACjB,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,MAAgB;IACjC,OAAO,MAAM,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;AACpE,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,GAAG,CAAC,MAAgB,EAAE,OAAmB,EAAE;IAC/D,MAAM,MAAM,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC;IACvC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;QAC3B,MAAM,IAAI,gBAAgB,CACxB,iCAAiC,MAAM,8BAA8B,EACrE,UAAU,CACX,CAAC;IACJ,CAAC;IAED,MAAM,QAAQ,GAAG,EAAE,CAAC,YAAY,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAC5C,MAAM,IAAI,GAAG,WAAW,CAAC;QACvB,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QAC/B,OAAO,EAAE,QAAQ;QACjB,OAAO,EAAE,QAAQ;QACjB,SAAS,EAAE,SAAS;QACpB,SAAS,EAAE,UAAU;KACtB,CAAC,CAAC;IAEH,eAAe;IACf,MAAM,YAAY,GAAG,mBAAmB,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,CAAC;IAC9D,IAAI,CAAC,YAAY,CAAC,EAAE,EAAE,CAAC;QACrB,MAAM,IAAI,gBAAgB,CACxB,+CAA+C,sBAAsB,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,EAC5F,OAAO,CACR,CAAC;IACJ,CAAC;IAED,sEAAsE;IACtE,4EAA4E;IAC5E,4DAA4D;IAC5D,MAAM,QAAQ,GAAG,aAAa,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,CAAC;IACpD,wEAAwE;IACxE,oEAAoE;IACpE,MAAM,cAAc,GAAG,cAAc,CAAC,QAAQ,EAAE;QAC9C,OAAO,EAAE,IAAI,CAAC,OAAO;QACrB,cAAc,EAAE,GAAG,EAAE,CAAC,IAAI;KAC3B,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC;IAEzC,kEAAkE;IAClE,qEAAqE;IACrE,wEAAwE;IACxE,8EAA8E;IAC9E,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAC;IACrC,IAAI,CAAC;QACH,MAAM,gBAAgB,GAAG,aAAa,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,CAAC;QAC5D,MAAM,cAAc,GAAG,cAAc,CAAC,gBAAgB,EAAE;YACtD,OAAO,EAAE,IAAI,CAAC,OAAO;YACrB,cAAc,EAAE,GAAG,EAAE,CAAC,IAAI;SAC3B,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC;QACzC,YAAY,GAAG,IAAI,GAAG,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC;IAC5F,CAAC;IAAC,MAAM,CAAC;QACP,wEAAwE;QACxE,4EAA4E;QAC5E,yEAAyE;QACzE,gEAAgE;IAClE,CAAC;IAED,MAAM,SAAS,GAAG,cAAc,CAAC,MAAM,CACrC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC,CACjE,CAAC;IACF,MAAM,iBAAiB,GAAG,cAAc,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CACpD,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC,CACzD,CAAC;IAEF,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACzB,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACtD,MAAM,IAAI,gBAAgB,CACxB,8CAA8C,KAAK,EAAE,EACrD,OAAO,CACR,CAAC;IACJ,CAAC;IAED,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,IAAI,iBAAiB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjC,MAAM,KAAK,GAAG,iBAAiB,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC9D,QAAQ,CAAC,IAAI,CACX,wBAAwB,iBAAiB,CAAC,MAAM,8FAA8F,KAAK,EAAE,CACtJ,CAAC;IACJ,CAAC;IAED,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC;IACtG,CAAC;IAED,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,aAAa,CAAC,CAAC;IAChE,MAAM,YAAY,CAAC,QAAQ,EAAE,GAAG,EAAE;QAChC,uEAAuE;QACvE,sEAAsE;QACtE,2EAA2E;QAC3E,6EAA6E;QAC7E,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAChD,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;QACvC,MAAM,OAAO,GAAG,mBAAmB,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC;QACrD,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC;YAChB,MAAM,IAAI,gBAAgB,CACxB,sEAAsE,sBAAsB,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,EAC9G,OAAO,CACR,CAAC;QACJ,CAAC;QACD,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAChC,CAAC,CAAC,CAAC;IAEH,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AACrG,CAAC"}

package/dist/cli/add/mutate.d.ts

@@ -8,6 +8,8 @@ export interface McpEntry {
         timeout_ms?: number;
     };
     enabled?: boolean;
+    min_version?: string;
+    version_command?: string[];
 }
 export interface CliEntry {
     name: string;

package/dist/cli/add/mutate.js.map

@@ -1 +1 @@
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package/dist/cli/adopt/derive.d.ts

@@ -3,12 +3,22 @@ export interface DerivedHook {
     event: string;
     command: string;
     match?: string;
+    /**
+     * settings.json hook `timeout`, captured verbatim (task 059b669c).
+     * apply emits `timeout: budget_ms` 1:1 (generate-settings.ts,
+     * toSettingsCommand), so carrying it back into `budget_ms` keeps the
+     * adopt→apply round-trip drift-free by construction. Deliberately NOT
+     * part of the drift key (`keyOf`): a timeout-only edit must not turn
+     * into an add-only "new hook" adoption of a duplicate entry.
+     */
+    timeout?: number;
 }
 export interface SettingsHookGroup {
     matcher?: string;
     hooks: {
         type?: string;
         command: string;
+        timeout?: number;
     }[];
 }
 export interface SettingsRoot {
@@ -50,7 +60,7 @@ export interface SettingsRootWithMcp extends SettingsRoot {
     mcpServers?: Record<string, SettingsMcpSpec>;
 }
 export declare function parseSettingsMcpServers(raw: unknown): DerivedMcp[];
-export declare function manifestMcpProjection(manifest: Manifest): DerivedMcp[];
+export declare function manifestMcpProjection(manifest: Manifest, homeDir?: string): DerivedMcp[];
 export type McpDriftReason = "new" | "modified";
 export interface McpDriftEntry {
     entry: DerivedMcp;

package/dist/cli/adopt/derive.js

@@ -1,3 +1,4 @@
+import { EVIDENCE_LEDGER_DB_ENV, GROUNDING_MCP_SERVER_NAME, groundingLedgerEnvValue, } from "../apply/generate-settings.js";
 const KNOWN_EVENTS = new Set([
     "SessionStart",
     "UserPromptSubmit",
@@ -37,10 +38,17 @@ export function parseSettingsHooks(raw) {
                     continue;
                 if (typeof h.command !== "string" || h.command.length === 0)
                     continue;
+                // Capture only values the manifest schema would accept
+                // (budget_ms: positive integer); anything else is ignored so a
+                // malformed hand-edit cannot poison the proposed manifest.
+                const timeout = typeof h.timeout === "number" && Number.isInteger(h.timeout) && h.timeout > 0
+                    ? h.timeout
+                    : undefined;
                 out.push({
                     event,
                     command: h.command,
                     ...(matcher !== undefined ? { match: matcher } : {}),
+                    ...(timeout !== undefined ? { timeout } : {}),
                 });
             }
         }
@@ -122,8 +130,26 @@ export function parseSettingsMcpServers(raw) {
     }
     return out;
 }
-export function manifestMcpProjection(manifest) {
-    return manifest.tools.mcp.map(toDerivedMcp);
+export function manifestMcpProjection(manifest, homeDir) {
+    const out = manifest.tools.mcp.map(toDerivedMcp);
+    // Mirror apply's grounding projection (generate-settings.ts,
+    // projectGroundingEnv): apply synthesizes EVIDENCE_LEDGER_DB onto the
+    // enabled grounding-mcp entry, so the manifest-side projection must
+    // carry the same key — otherwise every adopt after an apply reports
+    // phantom "modified" drift on grounding-mcp and, if applied, bakes the
+    // machine-specific absolute path into the shared manifest (task
+    // 129e1b94 review, MED finding).
+    const groundingManifestEntry = manifest.tools.mcp.find((m) => m.name === GROUNDING_MCP_SERVER_NAME);
+    const grounding = out.find((m) => m.name === GROUNDING_MCP_SERVER_NAME);
+    if (grounding !== undefined &&
+        groundingManifestEntry?.enabled !== false &&
+        !grounding.env?.[EVIDENCE_LEDGER_DB_ENV]) {
+        grounding.env = {
+            ...(grounding.env ?? {}),
+            [EVIDENCE_LEDGER_DB_ENV]: groundingLedgerEnvValue(manifest, homeDir),
+        };
+    }
+    return out;
 }
 function toDerivedMcp(m) {
     const command = Array.isArray(m.command)

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

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package/dist/cli/adopt/index.js

@@ -82,12 +82,9 @@ export async function adopt(settingsPath, opts = {}) {
     }
     const adoptedMcpNames = [];
     const replacedMcpNames = [];
-    // Preserve manifest-only fields (`health`, `enabled: false`) when
-    // replacing an existing entry. The settings.json projection only
-    // carries `command` + `env`; without this merge, hand-edits to those
-    // fields would silently wipe `health` (load-bearing for the audit /
-    // doctor / probe paths) and `enabled: false` (which would re-enable a
-    // server the user explicitly turned off).
+    // Preserve manifest-only fields when replacing an existing entry —
+    // `buildMcpEntry` is the single source of truth for exactly which
+    // fields are carried forward and why.
     const manifestByName = new Map(manifest.tools.mcp.map((m) => [m.name, m]));
     for (const m of mcpDrift) {
         if (m.reason === "modified")
@@ -203,24 +200,33 @@ function buildMcpEntry(d, existing) {
     };
     if (d.env && Object.keys(d.env).length > 0)
         entry.env = { ...d.env };
-    // Carry forward manifest-only fields. settings.json's mcpServers shape
-    // has no projection for `health` (used by doctor / probe / policy paths)
-    // or `enabled: false` (explicit opt-out the user chose to keep), so a
-    // pure replace from the projected drift would silently wipe them.
-    // `enabled: true` is the schema default and is omitted to keep the
-    // re-emitted YAML clean.
+    // Carry forward the manifest-only fields — exactly these four:
+    // `health` (doctor / probe / policy paths), `enabled: false` (explicit
+    // opt-out), `min_version` and `version_command` (doctor's version
+    // probe floor, task 059b669c). settings.json's mcpServers shape has no
+    // projection for any of them, so a pure replace from the projected
+    // drift would silently wipe them. `enabled: true` is the schema
+    // default and is omitted to keep the re-emitted YAML clean.
     if (existing) {
         if (existing.health)
             entry.health = { ...existing.health };
         if (existing.enabled === false)
             entry.enabled = false;
+        if (existing.min_version !== undefined)
+            entry.min_version = existing.min_version;
+        if (existing.version_command !== undefined) {
+            entry.version_command = [...existing.version_command];
+        }
     }
     return entry;
 }
 function buildHookEntry(name, d) {
     // Adopted hooks default to non-blocking so the captured entry doesn't
     // unexpectedly start gating tool calls. The user can promote to soft/hard
-    // explicitly if they want enforcement.
+    // explicitly if they want enforcement. (Blocking is harness-internal —
+    // settings.json has no equivalent field — so it is genuinely not
+    // inferable from the adopted source; `timeout` IS captured and becomes
+    // `budget_ms`, matching apply's 1:1 projection, task 059b669c.)
     const entry = {
         name,
         event: d.event,
@@ -229,6 +235,8 @@ function buildHookEntry(name, d) {
     };
     if (d.match !== undefined)
         entry.match = d.match;
+    if (d.timeout !== undefined)
+        entry.budget_ms = d.timeout;
     return entry;
 }
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
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package/dist/cli/apply/apply.js

@@ -46,7 +46,7 @@ import { GENERATED_DIRNAME, resolveGeneratedDir } from "../../io/generated-dir.j
 import { resolveHomeDir } from "../../runtime/home-dir.js";
 import { CODEX_GENERATED_HEADER_LINE, generateCodexConfig, } from "./generate-codex-config.js";
 import { generateMemoryIndex } from "./generate-memory-index.js";
-import { generateSettingsWithWarnings } from "./generate-settings.js";
+import { GROUNDING_MCP_SERVER_NAME, generateSettingsWithWarnings, } from "./generate-settings.js";
 import { planCodexConfigInstall, writeCodexConfigInstall, } from "./install-codex-config.js";
 export { GENERATED_DIRNAME };
 export const SETTINGS_BASENAME = "settings.json";
@@ -149,7 +149,7 @@ function buildExpectedFiles(manifest, opts, manifestPath) {
     // solution-acceptance hook command so producer and consumer agree on the
     // verdict directory. Without this, a manifest-declared override splits them
     // onto different dirs and the completion-gate can never see a verdict.
-    const groundingMcp = manifest.tools.mcp.find((m) => m.name === "grounding-mcp");
+    const groundingMcp = manifest.tools.mcp.find((m) => m.name === GROUNDING_MCP_SERVER_NAME);
     const groundingEnv = (groundingMcp?.env ?? {});
     const verdictDirOverride = groundingEnv["SOLUTION_VERDICT_DIR"];
     const solutionVerdictDir = typeof verdictDirOverride === "string" && verdictDirOverride.trim().length > 0
@@ -394,7 +394,35 @@ export async function apply(opts = {}) {
                 if (parseError !== null) {
                     throw new HarnessExitError(`cannot --merge into ${targetPath}: ${parseError}`, EX_NOINPUT);
                 }
-                const mergeResult = mergeSettings(parsed, generatedSettings);
+                // Provenance for the mcpServers deep merge: the server names
+                // harness wrote on the PREVIOUS apply. A name that was
+                // harness-written then but is absent from the current generated
+                // output was removed / disabled in the manifest and must leave
+                // the target too (enabled:false stays a kill switch); a name
+                // never harness-written is an operator hand-add and survives.
+                let previouslyGeneratedMcpNames;
+                const priorGenerated = lastApply?.files[SETTINGS_BASENAME]?.content;
+                if (priorGenerated !== undefined) {
+                    try {
+                        const prior = JSON.parse(priorGenerated);
+                        const mcp = prior["mcpServers"];
+                        if (mcp !== null && typeof mcp === "object" && !Array.isArray(mcp)) {
+                            previouslyGeneratedMcpNames = new Set(Object.keys(mcp));
+                        }
+                        else {
+                            previouslyGeneratedMcpNames = new Set();
+                        }
+                    }
+                    catch {
+                        // Corrupt .last-apply record: provenance unknown, fall back
+                        // to preserving unknown names (the conservative reading).
+                    }
+                }
+                const mergeResult = mergeSettings(parsed, generatedSettings, {
+                    ...(previouslyGeneratedMcpNames !== undefined
+                        ? { previouslyGeneratedMcpNames }
+                        : {}),
+                });
                 targetContent = serializeJson(mergeResult.merged);
                 targetMergeSummary = summarizeMerge(targetPath, mergeResult);
             }

package/dist/cli/apply/apply.js.map

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

@@ -1,5 +1,9 @@
 import type { Hook, Manifest, McpServer } from "../../schema/index.js";
 export declare const DEFAULT_BUDGET_MS = 30000;
+/** The manifest `tools.mcp[]` entry name that grounding enforcement keys off. */
+export declare const GROUNDING_MCP_SERVER_NAME = "grounding-mcp";
+/** The env var grounding-mcp's ledger-bridge reads for the evidence-ledger DB path. */
+export declare const EVIDENCE_LEDGER_DB_ENV = "EVIDENCE_LEDGER_DB";
 export interface SettingsHookCommand {
     type: "command";
     command: string;
@@ -35,8 +39,47 @@ export interface GenerateSettingsExtras {
      * the output so a no-op contribution doesn't pollute the JSON.
      */
     packPermissions?: SettingsPermissions;
+    /**
+     * Home directory used to expand `~/` in projected values (the
+     * grounding evidence-ledger path). Defaults to `os.homedir()`;
+     * injected by tests for determinism.
+     */
+    homeDir?: string;
 }
 export declare function generateSettings(manifest: Manifest): SettingsRoot;
 export declare function generateSettingsWithWarnings(manifest: Manifest, extras?: GenerateSettingsExtras): GenerateSettingsResult;
 export declare function buildMcpServers(entries: McpServer[], warnings: string[]): Record<string, SettingsMcpServer>;
+/**
+ * Wire the manifest's `grounding:` section into the grounding-mcp server
+ * entry (task 129e1b94, harness-review-2026-07-01/grounding-decorative).
+ *
+ * `grounding.evidence_ledger.path` becomes the `EVIDENCE_LEDGER_DB` env on
+ * the `tools.mcp[grounding-mcp]` entry — the exact variable grounding-mcp's
+ * ledger-bridge reads (agent-grounding
+ * packages/grounding-mcp/src/ledger-bridge.ts). This makes `grounding:` the
+ * section that CONFIGURES the grounding-mcp entry instead of a decorative
+ * namesake, resolving the naming collision the 2026-07-01 review flagged.
+ *
+ * Rules:
+ * - Projection only fires when a grounding-mcp entry exists; without one
+ *   there is no consumer (doctor surfaces that inertness separately).
+ * - An operator-declared `env.EVIDENCE_LEDGER_DB` on the entry wins — an
+ *   explicit override is never clobbered (doctor warns when it diverges
+ *   from `grounding.evidence_ledger.path`).
+ * - The projected value is `~`-expanded to an absolute path, so the
+ *   literal-tilde child-process footgun (agent-tasks/42d224a6, the very
+ *   warning above in buildMcpServers) cannot re-enter via this path.
+ * - `retention_days`, `policies_source`, and `session.*` stay RESERVED:
+ *   nothing consumes them yet (evidence-ledger has no retention pruning),
+ *   and projecting an env no server reads would be decorative again. See
+ *   the status comments in src/schema/grounding.ts.
+ */
+export declare function projectGroundingEnv(manifest: Manifest, mcp: Record<string, SettingsMcpServer>, homeDir?: string): void;
+/**
+ * The value apply projects for `EVIDENCE_LEDGER_DB`: the manifest's
+ * `grounding.evidence_ledger.path`, `~`-expanded to an absolute path.
+ * Shared with adopt's manifest→settings projection so the apply→adopt
+ * round-trip stays drift-free by construction.
+ */
+export declare function groundingLedgerEnvValue(manifest: Manifest, homeDir?: string): string;
 export declare function buildMemoryRouterHook(manifest: Manifest): Hook | null;