@lannguyensi/harness 0.5.0 → 0.6.0

package/CHANGELOG.md

@@ -5,6 +5,83 @@ 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/).
 
+## [Unreleased]
+
+## [0.6.0] - 2026-05-03
+
+**Headline: the Phase-5 adoption-blocker cycle closes end-to-end.**
+`harness apply` now writes directly into a Claude Code settings
+discovery path (`--target` + `--merge`), translates the manifest's
+`tools.mcp[]` into the settings.json `mcpServers` block (so a real
+`claude -p --settings <apply'd>` session actually loads them), prints
+a Next-steps hint that names the real wire-up commands instead of
+leaving adopters to guess, and `harness adopt` round-trips hand-edits
+to `mcpServers` back into the manifest. The full
+`apply → hand-edit → adopt → apply` cycle is byte-identical on the
+settings.json bytes.
+
+Operator note: no schema changes; `harness.lock` gains an optional
+`target` entry kind (additive). Existing `harness.lock` files without
+target entries continue to parse. The new flags on `apply` are all
+opt-in; the default invocation still writes to `harness.generated/`.
+Per-package version bumped from 0.5.0 to 0.6.0; this is the first
+minor release on the `@lannguyensi/harness` npm distribution. No
+operator action required beyond `npm i -g @lannguyensi/harness@0.6.0`
+on machines running the published binary.
+
+### Added
+
+- **`harness apply --target / --merge / --force`** (task `d38f6f91`, PR #58):
+  write the rendered settings.json directly into a Claude Code settings
+  discovery path (e.g. `.claude/settings.local.json` or
+  `~/.claude/settings.json`). `--merge` does a 3-way merge that replaces
+  harness-owned top-level keys (today: `hooks`, `mcpServers`) and preserves
+  everything else. `harness.lock` records the target sha so `validate
+  --check-lock` flags out-of-band edits. Closes the adoption blocker that
+  forced every adopter into a hand `cp` or per-invocation `--settings`.
+- **`apply` translates `tools.mcp[]` into the settings.json `mcpServers`
+  block** (task `62380337`, PR #59). The Phase 5 #1a caveat is closed:
+  `init.mcp_servers` in a `claude -p --settings <apply'd>` session now
+  contains the manifest's MCP entries. Disabled servers (`enabled: false`)
+  are omitted; warnings (not errors) cover entries that survive schema
+  but produce no runnable command. String-form commands with embedded
+  whitespace in paths must be expressed as the array form to preserve
+  token boundaries.
+- **`apply` prints a Next-steps hint after a successful run** (task
+  `517aa919`, PR #60). After the summary line, the CLI prints concrete,
+  copy-pasteable next actions: one-shot `claude -p --settings ...`,
+  project-scope `harness apply --target .claude/settings.local.json`,
+  and user-global `harness apply --target ~/.claude/settings.json --merge`.
+  When `--target` was actually written, the hint collapses to a single
+  verify line with `--settings <targetPath>` included (so non-canonical
+  target paths still resolve through `claude -p`). Two new flags pair
+  with this: `--quiet` suppresses the hint while keeping the summary,
+  and `--json` emits a machine-readable JSON summary instead of prose
+  (implies `--quiet`; refusal outcomes still set non-zero exit).
+  Motivated by a 2026-05-03 hallucination incident where an agent
+  fabricated a non-existent `claude -p --output-dir` flag because
+  nothing in the apply output guided the wire-up step; both unit and
+  CLI integration tests assert the hint never contains `--output-dir`.
+- **`adopt` reverse-projection for `mcpServers` into `tools.mcp[]`**
+  (task `7059d92b`, PR #61). Closes the round-trip gap: hand-edits to
+  settings.json's `mcpServers` block can now be captured back into the
+  manifest. New entries are appended; same-name entries with different
+  command/env are replaced (preserving manifest-only fields like `health`
+  and `enabled: false`, so adopting a hand-edit does not silently wipe
+  doctor/probe/policy metadata). The full
+  `harness apply --target ... --merge → hand-edit → harness adopt → harness apply`
+  cycle is byte-identical on the settings.json bytes.
+
+### Notes for upgraders
+
+- The settings.json output now includes a `mcpServers` key when your
+  manifest declares enabled MCP servers. On the first apply after
+  upgrade, the file grows by that block. The three-state compare handles
+  this safely (no spurious drift-refuse on the generated file), but if
+  you have hand-edited a `mcpServers` block into a previously apply'd
+  settings.json, the next apply will refuse (`drift-refuse`) until you
+  reconcile via `harness adopt` or `--overwrite-drift`.
+
 ## [0.5.0] - 2026-05-01
 
 **Phase 5: dogfood + polish.** Phase 4 shipped policies that fire; Phase 5

package/README.md

@@ -6,22 +6,39 @@ One zod-validated YAML manifest for grounding, tools, memory, hooks, and policie
 
 > Most config tools tell you what an agent is configured to use. `harness` tells you what an agent is *allowed to do*, under this exact context, and why.
 
-`harness` collapses the six-to-eight surfaces a working agent harness leaks across (`settings.json`, `CLAUDE.md`, memory frontmatter, MCP registrations, per-project overrides, hook scripts) into a single source of truth. Today (`v0.4.0`) policies fire end-to-end: a `mcp__agent-tasks__pull_requests_merge` call against a session without a `review:${PR_NUMBER}` ledger entry refuses; `harness explain review-before-merge --trace` shows exactly why. Phase 6 adds an *Understanding Gate* (agents confirm task interpretation before editing); Phase 7 adds a *Risk Gate* that blocks `DROP TABLE` against a prod target — even when the model would happily run it.
+`harness` collapses the six-to-eight surfaces a working agent harness leaks across (`settings.json`, `CLAUDE.md`, memory frontmatter, MCP registrations, per-project overrides, hook scripts) into a single source of truth. Today (`v0.5.0`) policies fire end-to-end: a `mcp__agent-tasks__pull_requests_merge` call against a session without a `review:${PR_NUMBER}` ledger entry refuses; `harness explain review-before-merge --trace` shows exactly why. Phase 6 adds an *Understanding Gate* (agents confirm task interpretation before editing); Phase 7 adds a *Risk Gate* that blocks `DROP TABLE` against a prod target, even when the model would happily run it.
+
+## Install
+
+```bash
+npm i -g @lannguyensi/harness
+```
+
+The CLI binary is `harness`. Node ≥ 20 required.
 
 ## Try it in 60 seconds
 
+```bash
+# Statically predict which policies fire for a tool call (no ledger, no LLM).
+# Uses the bundled reference manifest from the npm package.
+harness dry-run "merge PR 42" \
+  --tool mcp__agent-tasks__pull_requests_merge \
+  --tool-args '{"prNumber":42}' \
+  --config "$(npm root -g)/@lannguyensi/harness/dist/../docs/examples/full-manifest.yaml"
+```
+
+Or from a checkout:
+
 ```bash
 git clone https://github.com/LanNguyenSi/harness && cd harness
 npm install && npm run build
-
-# Statically predict which policies fire for a tool call (no ledger, no LLM)
 node dist/cli/main.js dry-run "merge PR 42" \
   --tool mcp__agent-tasks__pull_requests_merge \
   --tool-args '{"prNumber":42}' \
   --config docs/examples/full-manifest.yaml
 ```
 
-`dry-run` reads the reference manifest (`docs/examples/full-manifest.yaml`), runs the trigger matcher, substitutes `${PR_NUMBER}=42` through the JSONPath-restricted extract DSL, and tells you exactly which hooks would fire and which policies would match — before any ledger I/O.
+`dry-run` reads the reference manifest, runs the trigger matcher, substitutes `${PR_NUMBER}=42` through the JSONPath-restricted extract DSL, and tells you exactly which hooks would fire and which policies would match — before any ledger I/O.
 
 ## What a run looks like
 
@@ -72,10 +89,12 @@ When the matching policy actually fires (via `harness policy intercept`, wired b
 {"decision":"deny","reason":"review-before-merge: no matching ledger entry for tag `review:42`"}
 ```
 
+With `--verbose` (or `HARNESS_POLICY_VERBOSE=1`), stderr also carries a structured diagnostic block — policy name, ledger_tag, matched count, reason, sorted extract values — so the user sees *why* without a follow-up `explain --trace`.
+
 After the entry is recorded, the same call is silently allowed. Every fire writes a `policy_decision` row that `harness audit` and `harness explain --trace` replay:
 
 ```
-$ node dist/cli/main.js audit --since 1h --policy review-before-merge --session sess-1 --config docs/examples/full-manifest.yaml
+$ harness audit --since 1h --policy review-before-merge
 
 timestamp                 policy               outcome  reason
 ------------------------  -------------------  -------  ---------------------------------------------
@@ -83,6 +102,27 @@ timestamp                 policy               outcome  reason
 2026-04-30T18:31:00.000Z  review-before-merge  allow    1 matching ledger entries for tag `review:42`
 ```
 
+Inside a Claude Code session, `--session` defaults to `$CLAUDE_SESSION_ID`, so the read path automatically lines up with what the runtime hook wrote.
+
+## Wire into Claude Code
+
+By default, `harness apply` writes the rendered settings to `harness.generated/settings.json` next to your manifest. To make Claude Code actually use it, point `apply` at a settings discovery path with `--target`:
+
+```bash
+# Project scope: write straight to .claude/settings.local.json (created if missing).
+harness apply --target .claude/settings.local.json
+
+# User scope: merge harness-owned keys into your existing ~/.claude/settings.json,
+# preserving env, permissions, enabledPlugins, and any other top-level keys.
+harness apply --target ~/.claude/settings.json --merge
+```
+
+`--merge` does a 3-way merge: harness-owned top-level keys (today: `hooks`) get replaced wholesale; everything else in the existing target file is preserved verbatim. Re-applying is idempotent: running twice produces the same target, and the second run reports `no changes`.
+
+If the target exists and you pass neither `--merge` nor `--force`, apply refuses with a clear hint instead of clobbering. `--force` overwrites with the generated content as-is (no merge).
+
+`harness.lock` records the target path + a sha256 of the merged output, so `harness validate --check-lock` flags out-of-band edits.
+
 ## Next steps
 
 | If you want to... | Read |
@@ -96,14 +136,14 @@ timestamp                 policy               outcome  reason
 ## Common commands
 
 ```bash
-node dist/cli/main.js init --template full --config /tmp/harness-demo/harness.yaml
-node dist/cli/main.js describe   --config /tmp/harness-demo/harness.yaml --pillar tools
-node dist/cli/main.js doctor     --config /tmp/harness-demo/harness.yaml --shallow
-node dist/cli/main.js validate   --config /tmp/harness-demo/harness.yaml
-node dist/cli/main.js apply      --config /tmp/harness-demo/harness.yaml   # regenerate settings.json + MEMORY.md, write harness.lock
-node dist/cli/main.js diff --since-apply --config /tmp/harness-demo/harness.yaml
-node dist/cli/main.js explain review-before-merge --trace --config docs/examples/full-manifest.yaml
-node dist/cli/main.js audit --since 24h --config docs/examples/full-manifest.yaml
+harness init --template full --config /tmp/harness-demo/harness.yaml
+harness describe        --config /tmp/harness-demo/harness.yaml --pillar tools
+harness doctor          --config /tmp/harness-demo/harness.yaml --shallow
+harness validate        --config /tmp/harness-demo/harness.yaml
+harness apply           --config /tmp/harness-demo/harness.yaml   # regenerate settings.json + MEMORY.md, write harness.lock
+harness diff --since-apply --config /tmp/harness-demo/harness.yaml
+harness explain review-before-merge --trace
+harness audit --since 24h
 ```
 
 ## What's next
@@ -123,12 +163,12 @@ Both build on Phase 4's `policy intercept` runtime backbone; neither replaces it
 - [x] Repo bootstrap (LICENSE, .gitignore)
 - [x] README + VISION — repo legible
 - [x] ARCHITECTURE — YAML shape + CLI surface agreed
-- [x] ROADMAP — phases 1–4 with acceptance criteria
+- [x] ROADMAP — phases 1–7 with acceptance criteria
 - [x] Phase 1 — read-only inventory (`describe`, `validate`, `doctor`, `list`, `explain`, `diff`) — released as [`v0.1.0`](CHANGELOG.md#010---2026-04-29)
 - [x] Phase 2 — managed edits (`init`, `add`, `remove`, `adopt`, `export`) — released as [`v0.2.0`](CHANGELOG.md#020---2026-04-29)
 - [x] Phase 3 — declarative truth (`apply`, `diff --since-apply`, `harness.lock`) — released as [`v0.3.0`](CHANGELOG.md#030---2026-04-30)
 - [x] Phase 4 — policy layer (`policy intercept`, `explain --trace`, `audit`, `dry-run`, requires-evaluator + extract DSL + grounding-mcp adapter) — released as [`v0.4.0`](CHANGELOG.md#040---2026-04-30)
-- [ ] Phase 5 — polish + dogfood lessons (`apply --strict-lock`, `validate --check-lock`, sessionId default, `--verbose` deny diagnostics, sysexits normalisation, real-Claude-Code dogfood)
+- [x] Phase 5 — polish + dogfood lessons (`--verbose` policy diagnostics, `$CLAUDE_SESSION_ID` env fallback, server-side `audit` filter pushdown, `policy_decision` first-class entry type, audit `--since` UTC parse fix, `explain --trace` ms-precision sort, npm distribution as `@lannguyensi/harness`) — released as [`v0.5.0`](CHANGELOG.md#050---2026-05-01)
 - [ ] Phase 6 — Understanding Gate Policy Pack (agents must expose and confirm task understanding before write-capable tools fire)
 - [ ] Phase 7 — Risk Gate (Action Envelope + Risk Classifier + `allow / warn / require_approval / deny` for destructive-action prevention)
 
@@ -147,7 +187,7 @@ Our entry point into this problem: on 2026-04-23, an `agent-grounding` checkout
 - [`agent-tasks`](https://github.com/LanNguyenSi/agent-tasks) — the MCP-registered task platform whose registration + health appear in `harness describe`.
 - [`agent-preflight`](https://github.com/LanNguyenSi/agent-preflight) — local preflight validator; the canonical implementation of preflight-hook content harness wires (see `docs/ARCHITECTURE.md` §5 for the canonical hook-script shape and §6 for the Phase 4 policy that gates further work on a `preflight:${REPO}` ledger entry).
 - [`codebase-oracle`](https://github.com/LanNguyenSi/codebase-oracle) — one of the MCP surfaces being registered.
-- [`dev-tools`](https://github.com/LanNguyenSi/dev-tools) — `git-batch-cli`, a day-to-day tool whose inventory appears in `harness describe`.
+- [`agent-dx`](https://github.com/LanNguyenSi/agent-dx) — ships `git-batch-cli` (under `packages/git-batch-cli`), a day-to-day tool whose inventory appears in `harness describe`.
 
 ## License
 

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

@@ -26,6 +26,10 @@ export interface HookEntry {
 export type AddEntry = {
     type: "mcp";
     entry: McpEntry;
+} | {
+    type: "mcp_replace";
+    name: string;
+    entry: McpEntry;
 } | {
     type: "cli";
     entry: CliEntry;

package/dist/cli/add/mutate.js

@@ -1,10 +1,13 @@
-import { isSeq, parseDocument } from "yaml";
+import { isMap, isSeq, parseDocument } from "yaml";
 export function applyAdd(yamlText, action) {
     const doc = parseDocument(yamlText);
     switch (action.type) {
         case "mcp":
             addToSequence(doc, ["tools", "mcp"], action.entry);
             break;
+        case "mcp_replace":
+            replaceOrAppendByName(doc, ["tools", "mcp"], action.name, action.entry);
+            break;
         case "cli":
             addToSequence(doc, ["tools", "cli"], action.entry);
             break;
@@ -33,4 +36,30 @@ function addToSequence(doc, pathSegments, entry) {
     }
     throw new Error(`expected a YAML sequence at ${pathSegments.join(".")}, got ${typeof node}`);
 }
+// Find the first item in the sequence whose `name:` matches; replace it. If
+// no match is found, append (so the call site doesn't need to branch on
+// "exists vs new"). Comments and other YAML niceties on the original node are
+// dropped on replace; that is acceptable for the adopt round-trip use case
+// (the replacement is the user's hand-edit becoming the new source of truth).
+function replaceOrAppendByName(doc, pathSegments, name, entry) {
+    const node = doc.getIn(pathSegments);
+    if (node === undefined || node === null) {
+        doc.setIn(pathSegments, [entry]);
+        return;
+    }
+    if (!isSeq(node)) {
+        throw new Error(`expected a YAML sequence at ${pathSegments.join(".")}, got ${typeof node}`);
+    }
+    for (let i = 0; i < node.items.length; i++) {
+        const item = node.items[i];
+        if (!isMap(item))
+            continue;
+        const itemName = item.get("name");
+        if (typeof itemName === "string" && itemName === name) {
+            node.set(i, entry);
+            return;
+        }
+    }
+    node.add(entry);
+}
 //# sourceMappingURL=mutate.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"mutate.js","sourceRoot":"","sources":["../../../src/cli/add/mutate.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,aAAa,EAAiB,MAAM,MAAM,CAAC;AAmClE,MAAM,UAAU,QAAQ,CAAC,QAAgB,EAAE,MAAgB;IACzD,MAAM,GAAG,GAAG,aAAa,CAAC,QAAQ,CAAC,CAAC;IACpC,QAAQ,MAAM,CAAC,IAAI,EAAE,CAAC;QACpB,KAAK,KAAK;YACR,aAAa,CAAC,GAAG,EAAE,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;YACnD,MAAM;QACR,KAAK,aAAa;YAChB,qBAAqB,CAAC,GAAG,EAAE,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;YACxE,MAAM;QACR,KAAK,KAAK;YACR,aAAa,CAAC,GAAG,EAAE,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;YACnD,MAAM;QACR,KAAK,OAAO;YACV,aAAa,CAAC,GAAG,EAAE,CAAC,OAAO,EAAE,QAAQ,EAAE,SAAS,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;YACjE,MAAM;QACR,KAAK,MAAM;YACT,aAAa,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;YAC5C,MAAM;IACV,CAAC;IACD,6EAA6E;IAC7E,yEAAyE;IACzE,8EAA8E;IAC9E,kDAAkD;IAClD,OAAO,GAAG,CAAC,QAAQ,CAAC,EAAE,qBAAqB,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,EAAE,CAAC,CAAC;AACtE,CAAC;AAED,SAAS,aAAa,CACpB,GAAoB,EACpB,YAAsB,EACtB,KAAc;IAEd,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;IACrC,IAAI,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QACxC,GAAG,CAAC,KAAK,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC;QACjC,OAAO;IACT,CAAC;IACD,IAAI,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QAChB,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAChB,OAAO;IACT,CAAC;IACD,MAAM,IAAI,KAAK,CACb,+BAA+B,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,OAAO,IAAI,EAAE,CAC5E,CAAC;AACJ,CAAC;AAED,4EAA4E;AAC5E,wEAAwE;AACxE,8EAA8E;AAC9E,2EAA2E;AAC3E,8EAA8E;AAC9E,SAAS,qBAAqB,CAC5B,GAAoB,EACpB,YAAsB,EACtB,IAAY,EACZ,KAAc;IAEd,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;IACrC,IAAI,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QACxC,GAAG,CAAC,KAAK,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC;QACjC,OAAO;IACT,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,+BAA+B,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,OAAO,IAAI,EAAE,CAC5E,CAAC;IACJ,CAAC;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAC3B,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC;YAAE,SAAS;QAC3B,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;QAClC,IAAI,OAAO,QAAQ,KAAK,QAAQ,IAAI,QAAQ,KAAK,IAAI,EAAE,CAAC;YACtD,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;YACnB,OAAO;QACT,CAAC;IACH,CAAC;IACD,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;AAClB,CAAC"}

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

@@ -36,3 +36,26 @@ export declare function computeDrift(settingsHooks: DerivedHook[], manifestHooks
  * `adopted-hook` if the command has no recognisable basename.
  */
 export declare function synthesizeName(d: DerivedHook, taken: Set<string>): string;
+export interface DerivedMcp {
+    name: string;
+    command: string[];
+    env?: Record<string, string>;
+}
+export interface SettingsMcpSpec {
+    command?: unknown;
+    args?: unknown;
+    env?: unknown;
+}
+export interface SettingsRootWithMcp extends SettingsRoot {
+    mcpServers?: Record<string, SettingsMcpSpec>;
+}
+export declare function parseSettingsMcpServers(raw: unknown): DerivedMcp[];
+export declare function manifestMcpProjection(manifest: Manifest): DerivedMcp[];
+export type McpDriftReason = "new" | "modified";
+export interface McpDriftEntry {
+    entry: DerivedMcp;
+    reason: McpDriftReason;
+}
+export declare function computeMcpDrift(settingsMcp: DerivedMcp[], manifestMcp: DerivedMcp[]): McpDriftEntry[];
+export { mcpEqual };
+declare function mcpEqual(a: DerivedMcp, b: DerivedMcp): boolean;

package/dist/cli/adopt/derive.js

@@ -91,4 +91,89 @@ 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 [];
+    const out = [];
+    for (const [name, specRaw] of Object.entries(root.mcpServers)) {
+        if (!isRecord(specRaw))
+            continue;
+        const spec = specRaw;
+        if (typeof spec.command !== "string" || spec.command.length === 0)
+            continue;
+        const args = Array.isArray(spec.args)
+            ? spec.args.filter((a) => typeof a === "string")
+            : [];
+        const command = [spec.command, ...args];
+        const entry = { name, command };
+        if (isRecord(spec.env)) {
+            const env = {};
+            for (const [k, v] of Object.entries(spec.env)) {
+                if (typeof v === "string")
+                    env[k] = v;
+            }
+            if (Object.keys(env).length > 0)
+                entry.env = env;
+        }
+        out.push(entry);
+    }
+    return out;
+}
+export function manifestMcpProjection(manifest) {
+    return manifest.tools.mcp.map(toDerivedMcp);
+}
+function toDerivedMcp(m) {
+    const command = Array.isArray(m.command)
+        ? [...m.command]
+        : m.command
+            .trim()
+            .split(/\s+/)
+            .filter((t) => t.length > 0);
+    const out = { name: m.name, command };
+    if (m.env && Object.keys(m.env).length > 0)
+        out.env = { ...m.env };
+    return out;
+}
+export function computeMcpDrift(settingsMcp, manifestMcp) {
+    const byName = new Map(manifestMcp.map((m) => [m.name, m]));
+    const out = [];
+    for (const s of settingsMcp) {
+        const existing = byName.get(s.name);
+        if (!existing) {
+            out.push({ entry: s, reason: "new" });
+            continue;
+        }
+        if (mcpEqual(existing, s))
+            continue;
+        out.push({ entry: s, reason: "modified" });
+    }
+    return out;
+}
+export { mcpEqual };
+function mcpEqual(a, b) {
+    if (a.command.length !== b.command.length)
+        return false;
+    for (let i = 0; i < a.command.length; i++) {
+        if (a.command[i] !== b.command[i])
+            return false;
+    }
+    const aEnv = a.env ?? {};
+    const bEnv = b.env ?? {};
+    const ak = Object.keys(aEnv).sort();
+    const bk = Object.keys(bEnv).sort();
+    if (ak.length !== bk.length)
+        return false;
+    for (let i = 0; i < ak.length; i++) {
+        const ka = ak[i];
+        const kb = bk[i];
+        if (ka !== kb)
+            return false;
+        if (aEnv[ka] !== bEnv[kb])
+            return false;
+    }
+    return true;
+}
 //# sourceMappingURL=derive.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"derive.js","sourceRoot":"","sources":["../../../src/cli/adopt/derive.ts"],"names":[],"mappings":"AAEA,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC;IAC3B,cAAc;IACd,kBAAkB;IAClB,YAAY;IACZ,aAAa;IACb,MAAM;IACN,cAAc;IACd,YAAY;CACb,CAAC,CAAC;AAiBH;;;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,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;iBACrD,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,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,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,KAAK,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;QAC9D,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,qBAAqB,CAAC,QAAkB;IACtD,OAAO,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;AAC9C,CAAC;AAED,SAAS,YAAY,CAAC,CAAY;IAChC,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC;QACtC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC;QAChB,CAAC,CAAC,CAAC,CAAC,OAAO;aACN,IAAI,EAAE;aACN,KAAK,CAAC,KAAK,CAAC;aACZ,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IACnC,MAAM,GAAG,GAAe,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,EAAE,CAAC;IAClD,IAAI,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC;QAAE,GAAG,CAAC,GAAG,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;IACnE,OAAO,GAAG,CAAC;AACb,CAAC;AASD,MAAM,UAAU,eAAe,CAC7B,WAAyB,EACzB,WAAyB;IAEzB,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IAC5D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package/dist/cli/adopt/index.d.ts

@@ -9,11 +9,19 @@ export interface AdoptResult {
     manifestPath: string;
     settingsPath: string;
     driftCount: number;
+    /** Hook entries adopted (subset of driftCount). */
+    hookDriftCount: number;
+    /** MCP entries adopted (subset of driftCount). */
+    mcpDriftCount: number;
     /** The unified diff of the proposed change. Empty when nothing to adopt. */
     diff: string;
     applied: boolean;
-    /** Names synthesised for the new manifest entries. */
+    /** Names synthesised for the new hook entries. */
     adoptedNames: string[];
+    /** Names of MCP entries adopted (new) or replaced (modified). */
+    adoptedMcpNames: string[];
+    /** Names of MCP entries replaced (existed in manifest, content differed). */
+    replacedMcpNames: string[];
     /** Human-readable status: "no-drift" | "declined" | "applied". */
     outcome: "no-drift" | "declined" | "applied";
 }

package/dist/cli/adopt/index.js

@@ -10,7 +10,7 @@ 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, manifestProjection, parseSettingsHooks, synthesizeName, } from "./derive.js";
+import { computeDrift, computeMcpDrift, manifestMcpProjection, manifestProjection, parseSettingsHooks, parseSettingsMcpServers, synthesizeName, } from "./derive.js";
 const DEFAULT_BASENAME = "harness.yaml";
 const LOCK_BASENAME = ".harness.lock";
 function resolveManifestPath(opts) {
@@ -47,14 +47,21 @@ export async function adopt(settingsPath, opts = {}) {
     }
     const settingsHooks = parseSettingsHooks(settingsRaw);
     const drift = computeDrift(settingsHooks, projection);
-    if (drift.length === 0) {
+    const settingsMcp = parseSettingsMcpServers(settingsRaw);
+    const mcpProjection = manifestMcpProjection(manifest);
+    const mcpDrift = computeMcpDrift(settingsMcp, mcpProjection);
+    if (drift.length === 0 && mcpDrift.length === 0) {
         return {
             manifestPath,
             settingsPath,
             driftCount: 0,
+            hookDriftCount: 0,
+            mcpDriftCount: 0,
             diff: "",
             applied: false,
             adoptedNames: [],
+            adoptedMcpNames: [],
+            replacedMcpNames: [],
             outcome: "no-drift",
         };
     }
@@ -70,6 +77,25 @@ export async function adopt(settingsPath, opts = {}) {
             entry: buildHookEntry(name, d),
         });
     }
+    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).
+    const manifestByName = new Map(manifest.tools.mcp.map((m) => [m.name, m]));
+    for (const m of mcpDrift) {
+        if (m.reason === "modified")
+            replacedMcpNames.push(m.entry.name);
+        adoptedMcpNames.push(m.entry.name);
+        proposedYaml = applyAdd(proposedYaml, {
+            type: "mcp_replace",
+            name: m.entry.name,
+            entry: buildMcpEntry(m.entry, manifestByName.get(m.entry.name)),
+        });
+    }
     const diff = unifiedDiff({
         fileName: path.basename(manifestPath),
         oldText: originalYaml,
@@ -93,10 +119,14 @@ export async function adopt(settingsPath, opts = {}) {
             return {
                 manifestPath,
                 settingsPath,
-                driftCount: drift.length,
+                driftCount: drift.length + mcpDrift.length,
+                hookDriftCount: drift.length,
+                mcpDriftCount: mcpDrift.length,
                 diff,
                 applied: false,
                 adoptedNames,
+                adoptedMcpNames,
+                replacedMcpNames,
                 outcome: "declined",
             };
         }
@@ -123,6 +153,19 @@ export async function adopt(settingsPath, opts = {}) {
             next = applyAdd(next, { type: "hook", entry: buildHookEntry(name, d) });
             lockTaken.add(name);
         }
+        // MCP entries adopt as replace-or-append (keyed by name), so re-applying
+        // the same drift under the lock is naturally idempotent: the same name
+        // gets the same replacement. Use the freshly-read manifest's entries
+        // for the field-preservation merge, in case a concurrent adopt added
+        // health/enabled to the same name in between.
+        const lockedMcpByName = new Map(currentManifest.tools.mcp.map((m) => [m.name, m]));
+        for (const m of mcpDrift) {
+            next = applyAdd(next, {
+                type: "mcp_replace",
+                name: m.entry.name,
+                entry: buildMcpEntry(m.entry, lockedMcpByName.get(m.entry.name)),
+            });
+        }
         const recheck = validateBeforeWrite(parseYaml(next));
         if (!recheck.ok) {
             throw new HarnessExitError(`proposed manifest fails schema validation after lock acquisition:\n${formatValidationErrors(recheck.errors)}`, EX_FAIL);
@@ -132,13 +175,38 @@ export async function adopt(settingsPath, opts = {}) {
     return {
         manifestPath,
         settingsPath,
-        driftCount: drift.length,
+        driftCount: drift.length + mcpDrift.length,
+        hookDriftCount: drift.length,
+        mcpDriftCount: mcpDrift.length,
         diff,
         applied: true,
         adoptedNames,
+        adoptedMcpNames,
+        replacedMcpNames,
         outcome: "applied",
     };
 }
+function buildMcpEntry(d, existing) {
+    const entry = {
+        name: d.name,
+        command: [...d.command],
+    };
+    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.
+    if (existing) {
+        if (existing.health)
+            entry.health = { ...existing.health };
+        if (existing.enabled === false)
+            entry.enabled = false;
+    }
+    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

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

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