@lannguyensi/harness 0.7.0 → 0.8.1

package/CHANGELOG.md

@@ -7,6 +7,235 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.8.1] - 2026-05-11
+
+**Headline: policy-pack enforcement actually blocks now.** 0.8.0 shipped
+the runtime intercept, the ledger plumbing, and the manifest schema, but
+the deny path was effectively observability-only: Claude Code never
+honoured the hook output shape harness emitted, so a denied tool call
+proceeded to the MCP transport and only failed at the downstream
+service. Live verification on 2026-05-11 against
+`mcp__agent-tasks__pull_requests_merge` with no matching
+`review:${PR_NUMBER}` ledger entry confirmed the new build is refused
+at the hook layer, before reaching agent-tasks. Operators on 0.8.0
+should upgrade.
+
+### Changed
+
+- `harness policy intercept` now writes a one-line stderr diagnostic
+  when the manifest has policies but none of them matched the inbound
+  event, e.g. `no policy matched event hook_event_name=(missing)
+  tool_name="..." (registered policy events: PreToolUse). If probing
+  by hand, ensure stdin includes hook_event_name (...).`. Previously
+  the engine exited 0 with empty stdout in that case, so an operator
+  hand-probing the CLI without `hook_event_name` saw what looked like
+  "the policy did not load" while the real cause was just a stripped
+  trigger field. The hint fires unconditionally (not gated on
+  `--verbose`) and stdout is unchanged, so the Claude Code hook
+  contract is preserved. Also extends the `harness policy intercept`
+  command help with the documented stdin shape so the next operator
+  does not have to source-dive. (Tracked as `harness#4fef0e1f`.)
+
+### Fixed
+
+- `harness policy intercept` now emits a Claude Code hook output that
+  Claude Code actually honours as a deny. Previously the CLI wrote
+  `{"decision":"deny","reason":...}`, which Claude Code parsed as "no
+  recognised decision" (the documented top-level value is `"block"`,
+  not `"deny"`) and let the tool call proceed; the policy ran, the
+  `policy_decision` row landed in the ledger, but the agent still
+  merged. The new payload always carries the documented top-level
+  `decision: "block"` field, and for PreToolUse events it additionally
+  emits the `hookSpecificOutput.permissionDecision: "deny"` envelope
+  Claude Code 2.1+ prefers. Non-PreToolUse events (UserPromptSubmit,
+  PostToolUse, Stop, ...) get the top-level form only, since
+  `permissionDecision` is PreToolUse-only per Anthropic's hook
+  protocol. Repro for the regression was a
+  `mcp__agent-tasks__pull_requests_merge` call with no matching
+  `review:${PR_NUMBER}` ledger entry: it reached agent-tasks and 404'd
+  there instead of being blocked at the hook. The sibling
+  Understanding-Gate emitter at `src/cli/pack/hook-pre-tool-use.ts`
+  was unaffected; it already emits `decision: "block"`, though it does
+  not yet carry the modern envelope. (Tracked as `harness#2436d9bf`.)
+
+## [0.8.0] - 2026-05-10
+
+**Headline: Understanding-Gate Policy Pack, end-to-end.** Phase 6 lands
+the *Policy Pack* concept as a first-class harness unit: a reusable
+bundle of instruction template, hooks, policies, and permission
+profiles that ships under one name and is referenced from
+`harness.yaml` with one key. The first showcase pack,
+`understanding-before-execution`, forces an agent to expose its task
+interpretation, an Understanding Report, before any write-capable
+tool fires. The user confirms or corrects; only after explicit
+approval is recorded as evidence may the agent edit, run shell,
+commit, push, or open a PR. The pack ships across two runtimes
+(Claude Code and Codex), three permission profiles
+(`safe-start` / `implementation-after-approval` / `high-risk-grill-me`),
+a CLI surface (`harness pack add / remove / list`,
+`harness apply --runtime <runtime>`, `harness approve understanding`,
+`harness doctor --target codex`), and a synthetic-stdin dogfood smoke
+under `dogfood/phase6-6/` that exercises block, allow, capture, and
+approve round-trips without a real Codex binary.
+
+Operator note: no schema bump (still `version: 1`). New manifest blocks
+(`policy_packs:`, `permission_profiles:`) are additive and default to
+empty, so `0.7.0` manifests parse byte-identically. Manifests with the
+pack enabled need a one-time `harness apply` after upgrade so the new
+`harness pack hook pre-tool-use` blocker replaces the npm package's
+standalone bin in the rendered `settings.json`. Ensure `harness` is on
+`$PATH` (`npm i -g @lannguyensi/harness@0.8.0`) before the next session
+starts.
+
+### Added
+- Phase 6 #6 follow-up: `harness pack hook codex-stop` captures the
+  agent's Understanding Report into
+  `.understanding-gate/reports/<iso>-codex-<sessionhash>.json` with
+  `approvalStatus: "pending"`. Wire format on stdin accepts either
+  `last_assistant_message` directly or a `messages[]` array (the last
+  assistant entry is used). The parser recognises markdown headings,
+  bold labels, and plain colon-prefixed labels for the six report
+  fields (interpretation, assumptions, openQuestions, outOfScope,
+  risks, verificationPlan), with synonym support (Questions,
+  Exclusions, Validation). Failure modes (malformed input, missing
+  session id, unwritable reports dir, no recognisable fields)
+  resolve to exit 0 + a stderr diagnostic; capture must never block
+  the agent's stop path. The Codex pack now contributes a Stop hook
+  alongside UserPromptSubmit and PreToolUse. Closes agent-tasks
+  `adf356a0`.
+- Phase 6 #6 follow-up: `harness doctor --target codex` evaluates the
+  harness side of the Codex adapter (binary resolution, harness-managed
+  `harness.generated/codex/config.toml` presence + banner, contributed
+  `[[hooks.*]]` command resolution, and persisted-report directory
+  writability). Codex error/warning counts roll into the top-level
+  totals; `--json` adds a structured `codexTarget` block to the
+  `DoctorReport`. The default `harness doctor` invocation is
+  unchanged. Closes agent-tasks `125fd02b`.
+- Phase 6 #6: Codex adapter for the `understanding-before-execution`
+  policy pack. New CLI flag `harness apply --runtime codex` emits
+  `harness.generated/codex/config.toml` (TOML hook stanzas) instead of
+  `settings.json`; operators copy or include the generated TOML into
+  their own `~/.codex/config.toml`. Two new pack hook subcommands ship:
+  `harness pack hook codex-pre-tool-use` (PreToolUse blocker on
+  `apply_patch|Bash|shell`: exit 2 + reason on stderr when no source
+  has approved, exit 0 otherwise) and `harness pack hook
+  codex-user-prompt-submit` (instruction-template injector that emits
+  the Understanding-Gate prompt on stdout for Codex to prepend to
+  `additional_instructions`). The Codex blocker shares the
+  approval-check pipeline with the Claude Code blocker (ledger source
+  via grounding-mcp + persisted report under
+  `.understanding-gate/reports/`, either approves). Synthetic-stdin
+  smoke under `dogfood/phase6-6/` exercises block + allow paths
+  end-to-end without a Codex binary. `--target` is rejected with
+  `--runtime codex` (target wires Claude Code's `settings.json`, not
+  produced under codex). Phase 6 #6 follow-ups filed as separate
+  agent-tasks entries: `harness doctor --target codex` adapter-health
+  check; Codex Stop-equivalent for transcript capture; permission
+  profile translator into Codex's sandbox shape.
+- Phase 6 anchor: additive `policy_packs:` manifest block (schema-only;
+  no runtime behaviour yet). Each entry has `name`, `source`
+  (default `builtin`), `enabled`, optional `description`, and an
+  opaque `config:` record validated by the pack itself at resolve
+  time. Duplicate names rejected at parse time; `.strict()` rejects
+  unknown keys per entry. The block defaults to `[]` so manifests
+  written for `0.7.0` parse byte-identically.
+- `docs/policy-packs/understanding-before-execution.md`: canonical
+  documentation for the first Policy Pack, covering target
+  architecture, manifest reference, mode semantics, permission-profile
+  sketches, adapter notes for Claude Code / OpenCode / Codex, and the
+  two-source approval-state model (evidence-ledger tag for harnessed
+  sessions; persisted JSON report for solo `@lannguyensi/understanding-gate`
+  users). Phase 6 #2 through #6 will wire the surfaces this doc
+  describes; see `docs/ROADMAP.md` for the sub-task decomposition.
+- `docs/examples/full-manifest.yaml` carries the canonical
+  `understanding-before-execution` pack as a worked example; the
+  byte-for-byte `harness describe` golden test covers the resulting
+  output.
+- Phase 6 #2: `harness apply` now expands enabled `policy_packs[]`
+  entries into hook contributions and an operator audit copy. For the
+  builtin `understanding-before-execution` pack this writes three
+  namespaced hooks into the generated `settings.json`
+  (`UserPromptSubmit` injector, `Stop` capture, `PreToolUse` blocker
+  matching `Edit|Write|Bash`, all pointing at the
+  `@lannguyensi/understanding-gate` bins) and an audit copy at
+  `harness.generated/policy-packs/<name>/instructions.md`. Pack files
+  flow through the existing three-state-compare + lock pipeline, so
+  drift on the audit copy is caught by `harness apply` and surfaced in
+  `harness diff --since-apply`. `enabled: false` skips the pack
+  entirely. `harness validate` rejects an enabled pack with an
+  unrecognised source (only `builtin` resolves in v1) or an unknown
+  builtin name. Phase 6 #4 will add the harness-side ledger-aware
+  PreToolUse blocker; the standalone blocker shipped in
+  `@lannguyensi/understanding-gate@>=0.2.0` is already wired today.
+- Phase 6 #3: new `harness pack` CLI subtree for managing `policy_packs[]`
+  declaratively. `harness pack add <name>` performs a schema-validated
+  insert (rejects unknown source/name pre-flight, then the schema
+  superRefine catches duplicates). `harness pack remove <name>` is
+  reference-checked against `.last-apply`: it refuses without `--force`
+  when applied state is present, and `--force` removes the manifest
+  entry, deletes the on-disk pack files under
+  `harness.generated/policy-packs/<name>/`, and prunes the
+  corresponding `.last-apply` entries so a follow-up `harness apply`
+  reconverges in one step. `harness pack list [--enabled-only] [--json]`
+  prints a flat table or pipeable JSON.
+- Phase 6 #4: harness-side PreToolUse blocker + approve flow. The
+  `understanding-before-execution` pack now ships its `PreToolUse` hook
+  pointing at the new `harness pack hook pre-tool-use` runtime verb
+  (was: the npm package's standalone bin). The harness blocker is the
+  superset: it consults BOTH the evidence-ledger tag
+  `understanding-approved:${SESSION_ID}` (via grounding-mcp's
+  `ledger_summary`, canonical for harnessed sessions) AND the
+  persisted JSON report under `.understanding-gate/reports/` (fallback
+  for sessions without grounding-mcp wired). Either source approves;
+  neither blocks the tool call with a Claude-Code-shaped deny JSON
+  containing the actionable next step (`run \`harness approve
+  understanding\``). Failure modes (manifest unreadable, pack disabled,
+  no session id) resolve to allow with a stderr diagnostic, so the
+  Understanding Gate never bricks a session. Ledger matching filters
+  out `policy_decision` audit rows (typed and legacy-prefix backstop)
+  so a policy decision whose serialised reason field happens to
+  contain the approval substring cannot falsely approve.
+
+  **Breaking change for users with `understanding-before-execution`
+  enabled**: the regenerated `settings.json` calls `harness pack hook
+  pre-tool-use` instead of the npm bin. Run `harness apply` after
+  upgrading, and ensure `harness` is on `$PATH` (e.g.
+  `npm i -g @lannguyensi/harness`) before the next session starts.
+- New `harness approve understanding [--session <id>] [--reports-dir
+  <path>] [--approved-by <actor>]` CLI verb that round-trips both
+  approval sources: writes the `understanding-approved:${SESSION_ID}`
+  ledger tag via `grounding-mcp`'s `ledger_add` AND flips
+  `approvalStatus: "approved"` on the latest matching persisted JSON
+  report (atomic rewrite). A degraded ledger surfaces as a one-line
+  warning, not a hard failure, so a solo
+  `@lannguyensi/understanding-gate` user without `grounding-mcp` wired
+  still benefits from the persisted-report path.
+- New generic `runtime/ledger-add.ts` writer mirroring the structural
+  shape of `recordPolicyDecision` but exposed for non-policy-decision
+  fact rows. Used by `harness approve understanding`; available to any
+  future pack that wants to emit a session-tagged ledger entry without
+  encoding a policy-decision payload.
+- Phase 6 #5: permission profiles. New top-level `permission_profiles:`
+  manifest block (additive, defaults to `{}`), with three v1 builtins
+  bundled with the `understanding-before-execution` pack: `safe-start`
+  (pre-approval default), `implementation-after-approval` (post-
+  approval working profile), and `high-risk-grill-me` (high-friction
+  for security / infra surfaces). Selection via the pack's
+  `config.permission_profile`. Profile actions (`read` / `edit` /
+  `bash` / `commit` / `push` / `pr` / `deploy`) translate to Claude
+  Code's `permissions: { allow, ask, deny }` block at apply time;
+  the new translator emits canonical tool patterns
+  (`Edit`/`Write`/`MultiEdit` for `edit`, `Bash(git commit*)` for
+  `commit`, etc.). `limited` and `ask_or_deny` collapse onto `ask`
+  for v1 (Claude Code does not natively distinguish them); finer-
+  grained shaping is a Phase 6 #5 follow-up. When multiple packs
+  contribute permissions, the merge follows
+  deny-wins-over-ask-wins-over-allow precedence: a stricter intent
+  from any pack is not silently relaxed by a more permissive
+  sibling. Profiles compose with the Phase 6 #4 PreToolUse blocker:
+  the static permissions block is the always-applies floor, the
+  blocker handles the conditional approval gate on top.
+
 ## [0.7.0] - 2026-05-06
 
 **Headline: workflows-as-data and full-session audit forensics.** The

package/README.md

@@ -13,10 +13,14 @@ applies, audits, and *enforces*.
 `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 (`v0.7.0`) policies fire end-to-end: a
+source of truth. Today (`v0.8.1`) policies fire end-to-end and ship as
+reusable *Policy Packs*: a
 `mcp__agent-tasks__pull_requests_merge` call against a session
-without a `review:${PR_NUMBER}` ledger entry refuses; `harness
-explain review-before-merge --trace` shows exactly why.
+without a `review:${PR_NUMBER}` ledger entry refuses; an `Edit` /
+`apply_patch` against a session without an approved Understanding
+Report refuses; `harness explain --last --trace` shows exactly why.
+The Understanding Gate ships across both Claude Code and Codex
+runtimes via `harness apply --runtime <claude-code|codex>`.
 
 ## What harness does
 
@@ -106,24 +110,59 @@ would match, before any ledger I/O.
       blocks, `harness session-export`, `explain --last`, audience-
       specific docs surfaces, released as
       [`v0.7.0`](CHANGELOG.md#070---2026-05-06).
-- [ ] Phase 6, Understanding Gate Policy Pack: agents must expose and
-      confirm task understanding before write-capable tools fire.
+- [x] Phase 6, Understanding Gate Policy Pack: `policy_packs:`
+      manifest block, the canonical `understanding-before-execution`
+      pack, `harness pack add / remove / list`,
+      `harness apply --runtime <claude-code|codex>` with TOML config
+      output for Codex, three permission profiles
+      (`safe-start` / `implementation-after-approval` /
+      `high-risk-grill-me`), a harness-side PreToolUse blocker that
+      consults both the evidence-ledger tag and the persisted JSON
+      report, `harness approve understanding`,
+      `harness doctor --target codex`, and a Codex Stop-equivalent
+      that captures Understanding Reports into
+      `.understanding-gate/reports/`. Released as
+      [`v0.8.0`](CHANGELOG.md#080---2026-05-10).
 - [ ] Phase 7, Risk Gate: Action Envelope + Risk Classifier +
       `allow / warn / require_approval / deny` for destructive-action
       prevention.
 
-## What's next
+## Policy Packs (v0.8.1)
+
+A *Policy Pack* is a reusable bundle of instruction template, hooks,
+policies, and permission profiles that ships under one name and is
+referenced from `harness.yaml` with a single key. The first pack,
+`understanding-before-execution`, forces agents to expose and confirm
+their task interpretation before any write-capable tool fires.
+
+```yaml
+policy_packs:
+  - name: understanding-before-execution
+    config:
+      mode: grill_me                       # fast_confirm | grill_me | strict
+      permission_profile: safe-start       # safe-start | implementation-after-approval | high-risk-grill-me
+```
 
-Two structurally larger themes are queued after Phase 5's polish.
+Manage packs with `harness pack add / remove / list`. Apply against
+either runtime:
 
-**Phase 6, Understanding Gate.** Before an agent edits files, runs
-shell, commits, or opens a PR, it must produce an *Understanding
-Report* (its interpretation of the task: derived todos, acceptance
-criteria, assumptions, out-of-scope, risks). The user confirms,
-corrects, or "grills me until precise enough". Only after explicit
-approval is recorded in the evidence ledger may write-capable tools
-fire. Ships as the first `harness` *Policy Pack*: a reusable bundle
-of instruction template + hooks + policies + permission profiles.
+```sh
+harness apply --runtime claude-code        # default; writes harness.generated/settings.json
+harness apply --runtime codex              # writes harness.generated/codex/config.toml
+```
+
+Approve a session's Understanding Report via
+`harness approve understanding --session <id>` (round-trips both the
+evidence-ledger tag and the persisted JSON report). Verify the
+adapter wiring with `harness doctor --target codex` (`--json` for
+machine-readable). The full reference lives in
+[`docs/policy-packs/understanding-before-execution.md`](docs/policy-packs/understanding-before-execution.md);
+synthetic-stdin dogfood under
+[`dogfood/phase6-6/`](dogfood/phase6-6/run-smoke.sh) exercises the
+block / allow / capture / approve round-trip without a real Codex
+binary.
+
+## What's next
 
 **Phase 7, Risk Gate.** Today's policy model evaluates a rule per
 matching trigger and returns a binary block/allow. Phase 7 makes
@@ -138,8 +177,8 @@ Motivating use case: prevent `DROP TABLE users`, `kubectl delete
 namespace prod`, `terraform destroy` against an unverified production
 target, even if the model would have happily run them.
 
-Both build on Phase 4's `policy intercept` runtime backbone; neither
-replaces it.
+Phase 7 builds on Phase 4's `policy intercept` runtime backbone and
+Phase 6's Policy Pack distribution surface; neither is replaced.
 
 > Bring your favorite agent harness. Add governance.
 

package/dist/cli/apply/apply.d.ts

@@ -1,9 +1,11 @@
 import { type DriftedAsset } from "../../io/harness-lock.js";
 import { type ThreeStateVerdict } from "../../io/three-state.js";
+import { type Runtime } from "../../policy-packs/index.js";
 export declare const GENERATED_DIRNAME = "harness.generated";
 export declare const SETTINGS_BASENAME = "settings.json";
 export declare const MEMORY_BASENAME = "MEMORY.md";
 export declare const MANIFEST_BASENAME = "harness.yaml";
+export declare const CODEX_CONFIG_BASENAME = "codex/config.toml";
 export interface ApplyOptions {
     configPath?: string;
     homeDir?: string;
@@ -40,6 +42,17 @@ export interface ApplyOptions {
      * settings as-is. Mutually exclusive with --merge.
      */
     force?: boolean;
+    /**
+     * Phase 6 #6 — `--runtime <claude-code|codex>`. Selects which adapter
+     * shape policy-pack hooks expand into and which artefacts apply
+     * writes. Defaults to `claude-code` (settings.json output unchanged
+     * from previous releases). When set to `codex`, settings.json is NOT
+     * written; instead `harness.generated/codex/config.toml` carries the
+     * Codex adapter configuration. The two runtimes are mutually
+     * exclusive in a single apply for v1; cross-runtime applies are a
+     * future enhancement.
+     */
+    runtime?: Runtime;
     /** Test-injectable confirmation prompt; defaults to a stdin readline. */
     prompt?: (message: string) => Promise<string>;
 }

package/dist/cli/apply/apply.js

@@ -36,15 +36,18 @@ import { buildLastApply, readLastApply, sha256Hex, verifyLastApplyIntegrity, wri
 import { unifiedDiff } from "../../io/patch.js";
 import { emitRestartHints } from "../../io/restart-hints.js";
 import { compare } from "../../io/three-state.js";
+import { expandPolicyPacks, DEFAULT_RUNTIME } from "../../policy-packs/index.js";
 import { parseManifest } from "../../schema/index.js";
 import { EX_NOINPUT, HarnessExitError } from "../exit-codes.js";
 import { loadManifest } from "../loader.js";
+import { generateCodexConfig } from "./generate-codex-config.js";
 import { generateMemoryIndex } from "./generate-memory-index.js";
 import { generateSettingsWithWarnings } from "./generate-settings.js";
 export const GENERATED_DIRNAME = "harness.generated";
 export const SETTINGS_BASENAME = "settings.json";
 export const MEMORY_BASENAME = "MEMORY.md";
 export const MANIFEST_BASENAME = "harness.yaml";
+export const CODEX_CONFIG_BASENAME = "codex/config.toml";
 const DRIFT_HINT_MESSAGE = 'run "harness adopt <file>" to capture changes, or re-run with --overwrite-drift to discard them';
 function resolveManifestPath(opts) {
     if (opts.configPath)
@@ -111,18 +114,64 @@ async function readlinePrompt(message) {
     }
 }
 function buildExpectedFiles(manifest, opts) {
-    const settingsResult = generateSettingsWithWarnings(manifest);
-    const settings = `${JSON.stringify(settingsResult.root, null, 2)}\n`;
+    // Phase 6 #2: expand policy_packs[] into hook contributions + extra
+    // generated files BEFORE settings projection. Pack hooks flow through
+    // generate-settings unchanged (they're just additional Hook entries
+    // in the in-memory manifest), and pack files flow through the same
+    // three-state-compare + lock pipeline as settings.json / MEMORY.md.
+    const runtime = opts.runtime ?? DEFAULT_RUNTIME;
+    const packExpansion = expandPolicyPacks(manifest, runtime);
+    const augmentedManifest = packExpansion.hooks.length === 0
+        ? manifest
+        : { ...manifest, hooks: [...manifest.hooks, ...packExpansion.hooks] };
     const indexResult = generateMemoryIndex(manifest, {
         ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
         ...(opts.project !== undefined ? { projectName: opts.project } : {}),
     });
+    // Pack files emit in stable order (sorted by relativePath) so two
+    // applies of the same manifest write byte-identical .last-apply.
+    const packFiles = [...packExpansion.files]
+        .sort((a, b) => (a.relativePath < b.relativePath ? -1 : a.relativePath > b.relativePath ? 1 : 0))
+        .map((f) => ({ basename: f.relativePath, content: f.content }));
+    if (runtime === "codex") {
+        // Codex apply: emit Codex config artefact instead of settings.json.
+        // settings.json is Claude Code's contract and meaningless to Codex.
+        // MEMORY.md and pack instructions.md are runtime-agnostic and ship
+        // unchanged.
+        const codexConfig = generateCodexConfig(augmentedManifest);
+        const codexWarnings = [...codexConfig.warnings];
+        if (packExpansion.permissions) {
+            // Phase 6 #6: pack permission profiles project into Claude Code's
+            // settings.json `permissions` block. The codex generator does not
+            // yet consume them (Codex sandbox shaping is a follow-up); the
+            // contribution would otherwise vanish silently.
+            const totalPerms = packExpansion.permissions.allow.length +
+                packExpansion.permissions.ask.length +
+                packExpansion.permissions.deny.length;
+            if (totalPerms > 0) {
+                codexWarnings.push(`policy_packs contributed ${totalPerms} permission entr${totalPerms === 1 ? "y" : "ies"}; --runtime codex does not yet wire permissions into Codex's sandbox shape (filed as a Phase 6 #6 follow-up)`);
+            }
+        }
+        return {
+            files: [
+                { basename: CODEX_CONFIG_BASENAME, content: codexConfig.content },
+                { basename: MEMORY_BASENAME, content: indexResult.content },
+                ...packFiles,
+            ],
+            warnings: [...codexWarnings, ...indexResult.warnings, ...packExpansion.warnings],
+        };
+    }
+    const settingsResult = generateSettingsWithWarnings(augmentedManifest, {
+        ...(packExpansion.permissions && { packPermissions: packExpansion.permissions }),
+    });
+    const settings = `${JSON.stringify(settingsResult.root, null, 2)}\n`;
     return {
         files: [
             { basename: SETTINGS_BASENAME, content: settings },
             { basename: MEMORY_BASENAME, content: indexResult.content },
+            ...packFiles,
         ],
-        warnings: [...settingsResult.warnings, ...indexResult.warnings],
+        warnings: [...settingsResult.warnings, ...indexResult.warnings, ...packExpansion.warnings],
     };
 }
 function readOnDisk(filePath) {
@@ -220,6 +269,13 @@ export async function apply(opts = {}) {
     if (!targetPath && (opts.merge || opts.force)) {
         throw new HarnessExitError(`--${opts.merge ? "merge" : "force"} requires --target`, EX_NOINPUT);
     }
+    // Phase 6 #6: --target wires the generated settings.json into a
+    // Claude Code path. The runtime=codex branch does not produce
+    // settings.json at all, so the combination is incoherent. Reject
+    // early instead of writing a half-broken state.
+    if (targetPath && opts.runtime === "codex") {
+        throw new HarnessExitError("--target is incompatible with --runtime codex (target wires Claude Code's settings.json)", EX_NOINPUT);
+    }
     let targetContent;
     let targetMergeSummary;
     let targetChanged = false;

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

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

@@ -0,0 +1,6 @@
+import type { Manifest } from "../../schema/index.js";
+export interface CodexConfigResult {
+    content: string;
+    warnings: string[];
+}
+export declare function generateCodexConfig(manifest: Manifest): CodexConfigResult;