@lannguyensi/harness 0.23.2 → 0.24.1

package/CHANGELOG.md

@@ -7,6 +7,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.24.1] - 2026-05-19
+
+**Headline: post-migration Codex apply fix.** v0.24.0 dogfood found that `harness apply --runtime codex --install` refused on drift after a default claude-code apply had rewritten `.last-apply` without the prior `codex/config.toml` entry. Two helpers close the gap: forward-merge of orphan `.last-apply` entries across runtimes, and banner-prefix recovery of an on-disk harness-generated Codex artifact when the entry is missing. The `CODEX_GENERATED_HEADER_LINE` literal is now exported from `generate-codex-config.ts` (single source of truth) and pinned via a regression test so a future banner re-word can't silently disable recovery. **Operator action**: none. The next `harness apply --runtime codex --install` after upgrading to v0.24.1 auto-recovers; subsequent applies are idempotent no-ops. Operators still on v0.24.0 who hit drift-refuse can either upgrade to v0.24.1 or run `harness apply --runtime codex --install --overwrite-drift` once.
+
+### Fixed
+
+- **`harness apply --runtime codex` no longer refuses on post-migration drift when `.last-apply` was Claude-only** (agent-tasks/f3e09849, PR #216). Surfaced 2026-05-19 right after the v0.24.0 home-dir migration: an operator who ran `harness apply` (default claude-code) after `harness migrate-home` ended up with a `.last-apply` that listed only the claude-code expected files. The prior codex entry for `codex/config.toml` was dropped wholesale because each apply rewrote `.last-apply` from scratch with the current runtime's expected set only. A subsequent `harness apply --runtime codex --install` then hit drift-refuse against the existing harness-generated `codex/config.toml` on disk (which still embedded the legacy `~/.claude/.understanding-gate/reports` paths), because the three-state-compare saw `lastApplied=null + onDiskCurrent=<stale> + manifestExpected=<new>` and treated the stale file as operator hand-edits. Two complementary fixes in `src/cli/apply/apply.ts`: (1) `buildMergedLastApplyRecord` now preserves orphan-from-other-runtime entries from the previous `.last-apply` when writing a new one, so a default claude-code apply no longer drops the codex baseline; (2) `recoverMissingLastApplyContent` accepts an on-disk `codex/config.toml` whose first line matches `CODEX_GENERATED_HEADER_LINE` (the literal banner the Codex generator emits) as a recoverable baseline when `.last-apply` has no entry for it, unsticking operators who upgraded mid-flight without the merged record. The recovery branch is also wired into the no-changes path so a recovered baseline persists for the next apply. The `CODEX_GENERATED_HEADER_LINE` constant is exported from `generate-codex-config.ts` (single source of truth) and pinned via a regression test that asserts the generator's first line matches the recovery branch's expected literal, so a future banner re-word fails the test loud instead of silently disabling recovery. Two new regression tests cover (a) codex apply → claude-code apply → codex apply with no drift-refuse, (b) stale-codex-artefact recovery with full path-regeneration through `--install`.
+
+## [0.24.0] - 2026-05-19
+
+**Headline: Codex parity and runtime-neutral state root.** Four PRs all merged 2026-05-19. PR #211 fixes the Codex hook config schema to match Codex 0.131.0 (PascalCase event keys, nested command-hook arrays, `timeout` in seconds), closing a silent gap where `harness apply --runtime codex` emitted a TOML that current Codex no longer loads. PR #212 follows up with `harness apply --runtime codex --install`, which merges the generated hook block into a marked harness-managed region of `~/.codex/config.toml` so operators no longer copy-paste by hand. PR #213 makes `harness approve understanding` runtime-neutral: the Codex pre-tool-use blocker now stages `.pending-approval` (mirror of the Claude blocker since 33abc147), the session-id resolver gains `$CODEX_SESSION_ID` env and a fifth tier that reads the freshest persisted report's `sessionId` JSON field, and the no-session-id error text drops the Claude-only transcript-grep advice. PR #214 (this release's anchor) moves the harness state root from `~/.claude/` to runtime-neutral `~/.harness/` and adds `harness migrate-home` for one-shot migration; the legacy fallback survives the v0.24.x line and is targeted for deletion in v0.25.0. **Operator action**: run `harness apply --runtime codex --install` if you use Codex; run `harness migrate-home --apply` then `harness apply` to move your state into the new root.
+
+### Changed
+
+- **Harness operator-state moved from `~/.claude/` to runtime-neutral `~/.harness/`** (agent-tasks/e65decef, PR #214). v0.24.0's headline change. The harness's entire state root was historically hardcoded to `~/.claude/` (default manifest, generated artefacts, persisted reports, lockfile), a holdover from when Claude Code was the only first-class runtime. With Codex parity shipping in v0.23.x and v0.24.0, that naming was misleading for Codex-only operators and surface-area-breaking on a clean system with no Claude Code installed. The new resolver `resolveHomeDir()` (`src/runtime/home-dir.ts`) picks the state root from this precedence chain: explicit `--home` flag, `$HARNESS_HOME` env, existing `~/.harness/`, legacy `~/.claude/` (with a one-line stderr deprecation warning per process when harness state is detected there), create-on-first-use `~/.harness/`. A bare `~/.claude/` directory that contains only Claude Code's own `settings.json` does NOT trigger the legacy fallback: only the presence of `harness.yaml` or `harness.generated/` counts as evidence that harness state lives there, so we never accidentally write into Claude Code's runtime config dir. A new command `harness migrate-home` (dry-run by default, `--apply` to commit) atomically moves `harness.yaml` / `harness.generated/` / `.understanding-gate/` / `harness.lock` from the legacy root to the new root and drops a breadcrumb at `~/.claude/MOVED_TO_~_DOT_HARNESS.txt`. Re-running on already-migrated state is a clean no-op. The migration command refuses to overwrite an existing item at the new path. Subdirectory names inside the new root are unchanged from v0.23.x so the move is a plain `mv` per item, no schema or filename rewrites. The deprecation warning fires at most once per process. **Operator action**: run `harness migrate-home --apply` then `harness apply` to regenerate embedded paths (e.g. `UNDERSTANDING_GATE_REPORT_DIR` in `settings.json` hook commands). The legacy fallback is supported through the v0.24.x line; deletion is targeted for v0.25.0. Operator-facing sweeps in this release: `--config <path>` default-text now reads `~/.harness/harness.yaml; legacy fallback ~/.claude/harness.yaml` across all 33 subcommands; init template comments (`MINIMAL_TEMPLATE`, `FULL_TEMPLATE`, `SOLO_TEMPLATE`, `TEAM_TEMPLATE`) now lead with `~/.harness/harness.yaml`. Tests: 9 in `tests/runtime/home-dir.test.ts` cover full precedence + once-per-process warning + bare-`~/.claude/` non-claim, 7 in `tests/cli/migrate-home.test.ts` cover dry-run, apply, byte-for-byte preservation, idempotent re-run, target-conflict refuse, no-op on fresh install, and partial-migration recovery. New operator guide at `docs/migration/v0.24.0-home-dir.md`. The `resolvePaths` isolation guard from PR #199 is preserved symmetrically against both new and legacy paths; tests still need `homeDir` injection or `HARNESS_ALLOW_REAL_GENERATED_DIR=1` to fall back.
+
+### Added
+
+- **`harness approve understanding` resolves Codex sessions cleanly without `--session`** (agent-tasks/f608b4ee, PR #213). Two complementary fixes close the Codex approval-UX gap surfaced during the 2026-05-19 dogfood: (1) the Codex pre-tool-use blocker (`src/cli/pack/hook-codex-pre-tool-use.ts`) now calls `writePendingApproval(generatedDir, sessionId)` on the block path, mirroring the symmetric staging the Claude blocker has carried since task 33abc147, so arg-less `harness approve understanding` after a Codex PreToolUse block resolves via `.pending-approval` the same way it does in a Claude session; (2) session-id resolution in `src/cli/approve/understanding.ts` gains two new tiers: `$CODEX_SESSION_ID` env (peer of `$CLAUDE_SESSION_ID`, symmetric with the Codex hook's own fallback) and a fifth tier that reads the freshest persisted Understanding Report under `<reportsDir>` and pulls its JSON `sessionId` field. That fifth tier covers the post-Understanding-Report-pre-block window an operator hits when the agent has produced a report but no tool call has yet tripped the gate to stage `.pending-approval`: runtime-neutral, no env-var dependency, no log scraping. The no-session-id error text is rewritten: it now names both env vars, points the operator at the freshest report under the actual `<reportsDir>` as the canonical runtime-neutral recovery path, and drops the Claude-only `ls -t ~/.claude/projects/*/[0-9a-f]*.jsonl` advice that misled Codex operators. `sessionSource` discriminates `env-claude` / `env-codex` so the CLI annotation prints exactly which env var won (e.g. `session: <id> (from $CODEX_SESSION_ID)`). 6 new tests cover the $CODEX_SESSION_ID env tier, the Claude-over-Codex env precedence, the tier-5 newest-report fallback (including legacy reports without a sessionId field), tier-4 beating tier-5, and the rewritten error message; 4 new tests in `tests/cli/pack-hook-codex-pre-tool-use.test.ts` cover the staging-on-block / no-staging-on-allow / no-generatedDir / staging-write-throws contract. Note: the deeper `~/.claude/` to `~/.harness/` home-dir migration that prompted this task is tracked as a separate release vehicle (agent-tasks/e65decef, v0.24.0); this PR is the symptom-level fix the operator sees today.
+- **`harness apply --runtime codex --install` merges the generated hook block into `~/.codex/config.toml`** (agent-tasks/6167f326, PR #212). Codex applies previously stopped at writing `harness.generated/codex/config.toml`; the operator then had to copy/paste the harness-managed block into their active Codex config by hand. After PR #211 fixed the hook schema, that manual step also became the only way to actually take the fix live, which surfaced as dogfood friction on 2026-05-19. The installer closes that gap: a marked block (`# Harness Codex hook wiring.` source-prefix line + `# BEGIN harness-managed codex hooks` / `# END harness-managed codex hooks` fence) is replaced in-place, every byte outside the fence is preserved verbatim, and a timestamped backup (`<config>.harness-backup-<ISO8601>`) is written before any change. First install (no prior block) appends with a separating blank line, legacy paste-style blocks (`[[hooks.pre_tool_use]]` + `timeout_ms` + `blocking`) and an existing current managed block both upgrade in-place via `findManagedRange()` which keys off the source-prefix, the BEGIN/END fence, or the generated-banner header. Re-running with unchanged content is a true no-op (`changed: false`, no backup written, exit no-changes). `validateCodexManagedConfig()` runs before any write and refuses to install a payload that still carries legacy fields (`match =`, `timeout_ms =`, `blocking =`, lower-snake hook tables) or a current-shaped hook table missing the nested `hooks = [{ type = "command", command, timeout }]` array, so a generator regression cannot silently break the operator's config. `--install` is rejected without `--runtime codex` and a new `--codex-config <path>` overrides the default `~/.codex/config.toml` for non-default installs. The `init --interactive` wizard's codex wire-now path now uses the installer instead of printing copy-paste instructions; the wizard's recovery hint also updates to the new command. 11 tests in `tests/cli/apply/apply-codex-runtime.test.ts` cover install / legacy-upgrade / current-block-update / idempotency / backup / no-install-without-codex-runtime, plus updated `tests/cli/init-interactive.test.ts` assertions for the wizard's new wiring. **Operator action**: re-run `harness apply --runtime codex --install` once to lift the harness-managed block off the manual copy-paste workflow; subsequent applies of the same manifest are no-ops.
+
+### Fixed
+
+- **Codex hook config generation matches the Codex 0.131.0 schema** (agent-tasks/4b2b43a0, PR #211). `harness apply --runtime codex` previously emitted the legacy flat shape (`[[hooks.pre_tool_use]]` with `name`, `match`, `timeout_ms`, `blocking`, `description`) that Codex 0.131.0 no longer loads. After applying that config into `~/.codex/config.toml` and restarting Codex, gates did not fire: a real `exec_command` reached the shell with no `hook/started` / `hook/completed` evidence in `codex-tui.log`. Verified against the current OpenAI/Codex source (`codex-rs/config/src/hook_config.rs`): hook table keys must be PascalCase event names (`[[hooks.PreToolUse]]`, `[[hooks.UserPromptSubmit]]`, `[[hooks.Stop]]`, `[[hooks.SessionStart]]`, `[[hooks.PostToolUse]]`), the matcher field is `matcher` (not `match`), and each group carries a nested `hooks = [{ type = "command", command = "...", timeout = N }]` array with `timeout` in seconds (upstream `timeout_sec` is serde-renamed to `timeout`). Generator now converts `budget_ms` to seconds via `Math.max(1, Math.ceil(budget_ms / 1000))` (rounds up, never tightens an operator's declared budget) and drops the Harness-internal `name` / `blocking` / `description` fields entirely since Codex has no slot for them. `expandCodexHookMatchPattern()` is preserved unchanged, so the `apply_patch|Bash|shell|exec_command|functions.exec_command` matcher still intercepts unified-exec on `Bash`. Banner comments and `docs/policy-packs/understanding-before-execution.md` updated to describe the new shape. Doctor (`src/cli/doctor/codex.ts`) was already shape-agnostic (validates banner + binary on PATH, not field names) and required no change. Schema acceptance confirmed via `codex --strict-config -c 'hooks.PreToolUse=[{matcher="Bash",hooks=[{type="command",command="/bin/true",timeout=5}]}]' doctor --json` on Codex 0.131.0. **Operator action**: re-run `harness apply --runtime codex` to regenerate `harness.generated/codex/config.toml`, then merge the new stanzas into `~/.codex/config.toml` and restart Codex; the prior generated file produced silent hook drops.
+
 ## [0.23.2] - 2026-05-18
 
 **Headline: policy-gate hint clarification + smoke flake.** Three PRs all merged today. PR #206 + PR #207 close the silent-fail trap on ledger_add hints in policy `ux.run` and `producers[].example`: the prior form named the required content tag but NOT the `sessionId` parameter, so an operator binding `sessionId` to the tag UUID (the natural assumption since the tag literally contains the task / PR number / branch) saw the same opaque rejection repeated. The two PRs sweep both rendering surfaces plus the operator-facing doc-prose. PR #208 bumps a flaky smoke-test wall-clock assertion (4500ms to 7000ms) that under CI load caused `npm test` to occasionally fail and confused downstream `preflight run .` into a false `npm-test: fail` blocker. **Operator action**: re-run `harness apply` (or `harness init --force`) to regenerate `settings.json` with the updated policy hints.

package/dist/cli/add/index.js

@@ -1,8 +1,8 @@
 import * as fs from "node:fs";
-import * as os from "node:os";
 import * as path from "node:path";
 import { parse as parseYaml } from "yaml";
 import { atomicWriteFile } from "../../io/atomic-write.js";
+import { resolveHomeDir } from "../../runtime/home-dir.js";
 import { withFileLock } from "../../io/lock.js";
 import { unifiedDiff } from "../../io/patch.js";
 import { formatValidationErrors, validateBeforeWrite, } from "../../io/validate-before-write.js";
@@ -16,7 +16,7 @@ const LOCK_BASENAME = ".harness.lock";
 function resolveTargetPath(opts) {
     if (opts.configPath)
         return path.resolve(opts.configPath);
-    return path.join(opts.homeDir ?? path.join(os.homedir(), ".claude"), DEFAULT_BASENAME);
+    return path.join(resolveHomeDir({ ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}) }).path, DEFAULT_BASENAME);
 }
 function entryName(action) {
     return action.type === "skill" ? action.entry : action.entry.name;

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package/dist/cli/adopt/index.js

@@ -1,9 +1,9 @@
 import * as fs from "node:fs";
-import * as os from "node:os";
 import * as path from "node:path";
 import * as readline from "node:readline/promises";
 import { parse as parseYaml } from "yaml";
 import { atomicWriteFile } from "../../io/atomic-write.js";
+import { resolveHomeDir } from "../../runtime/home-dir.js";
 import { withFileLock } from "../../io/lock.js";
 import { unifiedDiff } from "../../io/patch.js";
 import { formatValidationErrors, validateBeforeWrite, } from "../../io/validate-before-write.js";
@@ -16,7 +16,7 @@ const LOCK_BASENAME = ".harness.lock";
 function resolveManifestPath(opts) {
     if (opts.configPath)
         return path.resolve(opts.configPath);
-    return path.join(opts.homeDir ?? path.join(os.homedir(), ".claude"), DEFAULT_BASENAME);
+    return path.join(resolveHomeDir({ ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}) }).path, DEFAULT_BASENAME);
 }
 async function defaultPrompt(message) {
     const rl = readline.createInterface({ input: process.stdin, output: process.stderr });

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cli/adopt/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,KAAK,QAAQ,MAAM,wBAAwB,CAAC;AACnD,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,EAAkB,MAAM,uBAAuB,CAAC;AACtE,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACzE,OAAO,EACL,YAAY,EACZ,eAAe,EACf,qBAAqB,EACrB,kBAAkB,EAClB,kBAAkB,EAClB,uBAAuB,EACvB,cAAc,GAGf,MAAM,aAAa,CAAC;AA+BrB,MAAM,gBAAgB,GAAG,cAAc,CAAC;AACxC,MAAM,aAAa,GAAG,eAAe,CAAC;AAEtC,SAAS,mBAAmB,CAAC,IAAkB;IAC7C,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,KAAK,UAAU,aAAa,CAAC,OAAe;IAC1C,MAAM,EAAE,GAAG,QAAQ,CAAC,eAAe,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACtF,IAAI,CAAC;QACH,OAAO,MAAM,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;IACpC,CAAC;YAAS,CAAC;QACT,EAAE,CAAC,KAAK,EAAE,CAAC;IACb,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,KAAK,CACzB,YAAoB,EACpB,OAAqB,EAAE;IAEvB,MAAM,YAAY,GAAG,mBAAmB,CAAC,IAAI,CAAC,CAAC;IAC/C,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,MAAM,IAAI,gBAAgB,CACxB,iCAAiC,YAAY,8BAA8B,EAC3E,UAAU,CACX,CAAC;IACJ,CAAC;IACD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;QACjC,MAAM,IAAI,gBAAgB,CACxB,sCAAsC,YAAY,EAAE,EACpD,UAAU,CACX,CAAC;IACJ,CAAC;IAED,MAAM,YAAY,GAAG,EAAE,CAAC,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC;IAC3D,MAAM,QAAQ,GAAG,aAAa,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC;IACxD,MAAM,UAAU,GAAG,kBAAkB,CAAC,QAAQ,CAAC,CAAC;IAEhD,IAAI,WAAoB,CAAC;IACzB,IAAI,CAAC;QACH,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC,CAAC;IAClE,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,IAAI,gBAAgB,CACxB,iBAAiB,YAAY,uBAAwB,CAAW,CAAC,OAAO,EAAE,EAC1E,OAAO,CACR,CAAC;IACJ,CAAC;IAED,MAAM,aAAa,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAC;IACtD,MAAM,KAAK,GAAG,YAAY,CAAC,aAAa,EAAE,UAAU,CAAC,CAAC;IAEtD,MAAM,WAAW,GAAG,uBAAuB,CAAC,WAAW,CAAC,CAAC;IACzD,MAAM,aAAa,GAAG,qBAAqB,CAAC,QAAQ,CAAC,CAAC;IACtD,MAAM,QAAQ,GAAG,eAAe,CAAC,WAAW,EAAE,aAAa,CAAC,CAAC;IAE7D,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChD,OAAO;YACL,YAAY;YACZ,YAAY;YACZ,UAAU,EAAE,CAAC;YACb,cAAc,EAAE,CAAC;YACjB,aAAa,EAAE,CAAC;YAChB,IAAI,EAAE,EAAE;YACR,OAAO,EAAE,KAAK;YACd,YAAY,EAAE,EAAE;YAChB,eAAe,EAAE,EAAE;YACnB,gBAAgB,EAAE,EAAE;YACpB,OAAO,EAAE,UAAU;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IACzD,MAAM,YAAY,GAAa,EAAE,CAAC;IAClC,IAAI,YAAY,GAAG,YAAY,CAAC;IAChC,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;QACtB,MAAM,IAAI,GAAG,cAAc,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;QACtC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAChB,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACxB,YAAY,GAAG,QAAQ,CAAC,YAAY,EAAE;YACpC,IAAI,EAAE,MAAM;YACZ,KAAK,EAAE,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC;SAC/B,CAAC,CAAC;IACL,CAAC;IAED,MAAM,eAAe,GAAa,EAAE,CAAC;IACrC,MAAM,gBAAgB,GAAa,EAAE,CAAC;IACtC,kEAAkE;IAClE,iEAAiE;IACjE,qEAAqE;IACrE,oEAAoE;IACpE,sEAAsE;IACtE,0CAA0C;IAC1C,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IAC3E,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;QACzB,IAAI,CAAC,CAAC,MAAM,KAAK,UAAU;YAAE,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACjE,eAAe,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACnC,YAAY,GAAG,QAAQ,CAAC,YAAY,EAAE;YACpC,IAAI,EAAE,aAAa;YACnB,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI;YAClB,KAAK,EAAE,aAAa,CAAC,CAAC,CAAC,KAAK,EAAE,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;SAChE,CAAC,CAAC;IACL,CAAC;IAED,MAAM,IAAI,GAAG,WAAW,CAAC;QACvB,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC;QACrC,OAAO,EAAE,YAAY;QACrB,OAAO,EAAE,YAAY;QACrB,SAAS,EAAE,SAAS;QACpB,SAAS,EAAE,UAAU;KACtB,CAAC,CAAC;IAEH,+EAA+E;IAC/E,qEAAqE;IACrE,4EAA4E;IAC5E,4EAA4E;IAC5E,6EAA6E;IAC7E,MAAM,UAAU,GAAG,mBAAmB,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC;IAChE,IAAI,CAAC,UAAU,CAAC,EAAE,EAAE,CAAC;QACnB,MAAM,IAAI,gBAAgB,CACxB,+CAA+C,sBAAsB,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,EAC1F,OAAO,CACR,CAAC;IACJ,CAAC;IAED,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC;QACd,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,IAAI,aAAa,CAAC;QAC9C,MAAM,MAAM,GAAG,CAAC,MAAM,QAAQ,CAAC,GAAG,IAAI,iBAAiB,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QAC/E,IAAI,MAAM,KAAK,GAAG,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;YACvC,OAAO;gBACL,YAAY;gBACZ,YAAY;gBACZ,UAAU,EAAE,KAAK,CAAC,MAAM,GAAG,QAAQ,CAAC,MAAM;gBAC1C,cAAc,EAAE,KAAK,CAAC,MAAM;gBAC5B,aAAa,EAAE,QAAQ,CAAC,MAAM;gBAC9B,IAAI;gBACJ,OAAO,EAAE,KAAK;gBACd,YAAY;gBACZ,eAAe;gBACf,gBAAgB;gBAChB,OAAO,EAAE,UAAU;aACpB,CAAC;QACJ,CAAC;IACH,CAAC;IAED,MAAM,QA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package/dist/cli/apply/apply.d.ts

@@ -54,6 +54,16 @@ export interface ApplyOptions {
      * future enhancement.
      */
     runtime?: Runtime;
+    /**
+     * `--install` with `--runtime codex`: merge the generated Codex hook
+     * stanzas into the active Codex config as a marked harness-managed
+     * block. The installer preserves every byte outside that block.
+     */
+    installCodex?: boolean;
+    /** Override the active Codex config path for --runtime codex --install. */
+    codexConfigPath?: string;
+    /** Test-injectable clock for timestamped Codex config backups. */
+    now?: Date;
     /** Test-injectable confirmation prompt; defaults to a stdin readline. */
     prompt?: (message: string) => Promise<string>;
 }
@@ -67,6 +77,13 @@ export interface FileApplyOutcome {
     /** True when `expected !== onDiskCurrent` (whether or not we wrote). */
     changed: boolean;
 }
+export interface CodexConfigInstallOutcome {
+    configPath: string;
+    changed: boolean;
+    written: boolean;
+    summary: string;
+    backupPath?: string;
+}
 export interface ApplyResult {
     manifestPath: string;
     generatedDir: string;
@@ -101,6 +118,8 @@ export interface ApplyResult {
      * Present when --merge succeeded against an existing target.
      */
     targetMergeSummary?: string;
+    /** Present when --runtime codex --install was requested. */
+    codexConfigInstall?: CodexConfigInstallOutcome;
 }
 declare const DRIFT_HINT_MESSAGE = "run \"harness adopt <file>\" to capture changes, or re-run with --overwrite-drift to discard them";
 export declare function apply(opts?: ApplyOptions): Promise<ApplyResult>;

package/dist/cli/apply/apply.js

@@ -42,19 +42,28 @@ import { parseManifest } from "../../schema/index.js";
 import { EX_NOINPUT, HarnessExitError } from "../exit-codes.js";
 import { loadManifest } from "../loader.js";
 import { GENERATED_DIRNAME, resolveGeneratedDir } from "../../io/generated-dir.js";
-import { generateCodexConfig } from "./generate-codex-config.js";
+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 { planCodexConfigInstall, writeCodexConfigInstall, } from "./install-codex-config.js";
 export { GENERATED_DIRNAME };
 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';
+// Pinned to the same literal the Codex generator emits as line 1.
+// Single source of truth lives in generate-codex-config.ts so a future
+// banner re-word can't silently disable last-apply baseline recovery.
+const CODEX_GENERATED_HEADER = CODEX_GENERATED_HEADER_LINE;
 function resolveManifestPath(opts) {
     if (opts.configPath)
         return path.resolve(opts.configPath);
-    return path.join(opts.homeDir ?? path.join(os.homedir(), ".claude"), MANIFEST_BASENAME);
+    const home = resolveHomeDir({
+        ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
+    }).path;
+    return path.join(home, MANIFEST_BASENAME);
 }
 function resolveTargetPath(target, homeDir) {
     let p = target;
@@ -93,6 +102,17 @@ function readTargetJson(targetPath) {
 function serializeJson(obj) {
     return `${JSON.stringify(obj, null, 2)}\n`;
 }
+function codexInstallOutcome(result) {
+    return {
+        configPath: result.configPath,
+        changed: result.changed,
+        written: "written" in result ? result.written : false,
+        summary: result.summary,
+        ...("backupPath" in result && result.backupPath !== undefined
+            ? { backupPath: result.backupPath }
+            : {}),
+    };
+}
 // Prompts must survive `harness apply | tee log` (the user still needs to
 // see the question even when stdout is piped), so we write to stderr and
 // read from stdin. Don't "fix" this back to stdout.
@@ -209,7 +229,37 @@ function buildPrevManifestForHints(record) {
         return null;
     }
 }
+function recoverMissingLastApplyContent(basename, onDisk) {
+    // Runtime-specific applies share one harness.generated/.last-apply file.
+    // A default claude-code apply from older versions can leave an existing
+    // harness-generated Codex artefact on disk while dropping its last-apply
+    // entry. Treat only the Codex generator's own DO-NOT-EDIT artefact as a
+    // recoverable baseline; arbitrary files without a last-apply record still
+    // refuse as operator-owned drift.
+    if (basename !== CODEX_CONFIG_BASENAME || onDisk === null)
+        return null;
+    return onDisk.startsWith(CODEX_GENERATED_HEADER) ? onDisk : null;
+}
+function buildMergedLastApplyRecord(expected, previous, manifest, memoryDirSnapshots) {
+    const next = buildLastApply(Object.fromEntries(expected.map((f) => [f.basename, f.content])));
+    if (previous !== null) {
+        for (const [relPath, entry] of Object.entries(previous.files)) {
+            if (next.files[relPath] === undefined)
+                next.files[relPath] = entry;
+        }
+    }
+    const manifestSnapshotJson = JSON.stringify(manifest);
+    next.manifest = {
+        sha256: sha256Hex(manifestSnapshotJson),
+        content: manifestSnapshotJson,
+    };
+    if (Object.keys(memoryDirSnapshots).length > 0) {
+        next.memoryDirs = memoryDirSnapshots;
+    }
+    return next;
+}
 export async function apply(opts = {}) {
+    const runtime = opts.runtime ?? DEFAULT_RUNTIME;
     const manifestPath = resolveManifestPath(opts);
     if (!fs.existsSync(manifestPath)) {
         throw new HarnessExitError(`harness manifest not found at ${manifestPath}; run \`harness init\` first`, EX_NOINPUT);
@@ -226,6 +276,9 @@ export async function apply(opts = {}) {
     const { manifest } = loadManifest(loaderOpts);
     const { files: expected, warnings } = buildExpectedFiles(manifest, opts, manifestPath);
     const lastApply = readLastApply(generatedDir);
+    if (opts.installCodex && runtime !== "codex") {
+        throw new HarnessExitError("--install requires --runtime codex", EX_NOINPUT);
+    }
     // Asset-content drift detection (Phase 3 #6): if a previous apply wrote
     // harness.lock, re-hash every locked asset / memory-dir Merkle and report
     // mismatches. Warn-only: apply still proceeds and the lock is rewritten
@@ -338,13 +391,39 @@ export async function apply(opts = {}) {
             targetChanged = currentTargetContent !== targetContent;
         }
     }
+    let codexInstallPlan;
+    let codexInstallChanged = false;
+    if (opts.installCodex) {
+        const codexExpected = expected.find((f) => f.basename === CODEX_CONFIG_BASENAME);
+        if (!codexExpected) {
+            throw new HarnessExitError("internal: codex/config.toml missing from expected files", EX_NOINPUT);
+        }
+        codexInstallPlan = planCodexConfigInstall({
+            ...(opts.codexConfigPath !== undefined
+                ? { configPath: resolveTargetPath(opts.codexConfigPath) }
+                : {}),
+            ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
+            generatedPath: path.join(generatedDir, CODEX_CONFIG_BASENAME),
+            generatedContent: codexExpected.content,
+            ...(opts.now !== undefined ? { now: opts.now } : {}),
+        });
+        codexInstallChanged = codexInstallPlan.changed;
+    }
     const fileOutcomes = [];
     let anyDriftRefuse = false;
     let anyChanged = false;
+    let recoveredMissingLastApply = false;
     for (const f of expected) {
         const target = path.join(generatedDir, f.basename);
         const onDisk = readOnDisk(target);
-        const lastAppliedContent = lastApply?.files[f.basename]?.content ?? null;
+        let lastAppliedContent = lastApply?.files[f.basename]?.content ?? null;
+        if (lastAppliedContent === null) {
+            const recovered = recoverMissingLastApplyContent(f.basename, onDisk);
+            if (recovered !== null) {
+                lastAppliedContent = recovered;
+                recoveredMissingLastApply = true;
+            }
+        }
         const verdict = compare({
             manifestExpected: f.content,
             lastApplied: lastAppliedContent,
@@ -371,7 +450,7 @@ export async function apply(opts = {}) {
         fileOutcomes.push(outcome);
     }
     if (anyDriftRefuse && !opts.overwriteDrift) {
-        return {
+        const result = {
             manifestPath,
             generatedDir,
             files: fileOutcomes,
@@ -383,6 +462,9 @@ export async function apply(opts = {}) {
             dryRun: opts.dryRun ?? false,
             lockPath,
         };
+        if (codexInstallPlan)
+            result.codexConfigInstall = codexInstallOutcome(codexInstallPlan);
+        return result;
     }
     if (anyDriftRefuse && opts.overwriteDrift) {
         const promptFn = opts.prompt ?? readlinePrompt;
@@ -390,7 +472,7 @@ export async function apply(opts = {}) {
         // Case-insensitive comparison: a user typing `YES` or `Yes` is clearly
         // confirming. We still reject `y` per spec ("literal yes, not y").
         if (answer.trim().toLowerCase() !== "yes") {
-            return {
+            const result = {
                 manifestPath,
                 generatedDir,
                 files: fileOutcomes,
@@ -402,6 +484,9 @@ export async function apply(opts = {}) {
                 dryRun: opts.dryRun ?? false,
                 lockPath,
             };
+            if (codexInstallPlan)
+                result.codexConfigInstall = codexInstallOutcome(codexInstallPlan);
+            return result;
         }
         // Confirmed: continue to the write phase. The per-file `verdict` field
         // remains `drift-refuse` so callers can still see which files would
@@ -418,7 +503,7 @@ export async function apply(opts = {}) {
             files: fileOutcomes,
             warnings,
             restartHints,
-            outcome: anyChanged || targetChanged ? "would-apply" : "no-changes",
+            outcome: anyChanged || targetChanged || codexInstallChanged ? "would-apply" : "no-changes",
             lockDrift,
             written: false,
             dryRun: true,
@@ -430,9 +515,11 @@ export async function apply(opts = {}) {
             if (targetMergeSummary !== undefined)
                 result.targetMergeSummary = targetMergeSummary;
         }
+        if (codexInstallPlan)
+            result.codexConfigInstall = codexInstallOutcome(codexInstallPlan);
         return result;
     }
-    if (!anyChanged && !targetChanged && lastApply !== null) {
+    if (!anyChanged && !targetChanged && !codexInstallChanged && lastApply !== null) {
         // Idempotent no-op for generated files. If asset-content drift was
         // detected against harness.lock, rewrite the lock now with current
         // SHAs so the drift is not "sticky": the user sees the drift line
@@ -447,6 +534,13 @@ export async function apply(opts = {}) {
             const refreshedWithTarget = appendTargetEntry(refreshed, targetPath, targetContent, previousLock);
             writeLock(lockPath, refreshedWithTarget);
         }
+        if (recoveredMissingLastApply) {
+            const refreshedMemoryDirs = collectMemoryDirSnapshots(buildLockEntries(manifest, {
+                ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
+                ...(opts.project !== undefined ? { projectName: opts.project } : {}),
+            }));
+            writeLastApply(generatedDir, buildMergedLastApplyRecord(expected, lastApply, manifest, refreshedMemoryDirs));
+        }
         const result = {
             manifestPath,
             generatedDir,
@@ -463,6 +557,8 @@ export async function apply(opts = {}) {
             result.targetPath = targetPath;
             result.targetWritten = false;
         }
+        if (codexInstallPlan)
+            result.codexConfigInstall = codexInstallOutcome(codexInstallPlan);
         return result;
     }
     // Only write generated files if anything in harness.generated/ actually
@@ -498,19 +594,19 @@ export async function apply(opts = {}) {
         atomicWriteFile(targetPath, targetContent);
         targetWritten = true;
     }
+    let codexInstallResult;
+    if (codexInstallPlan && codexInstallPlan.changed) {
+        codexInstallResult = writeCodexConfigInstall(codexInstallPlan, {
+            ...(opts.now !== undefined ? { now: opts.now } : {}),
+        });
+    }
+    else if (codexInstallPlan) {
+        codexInstallResult = { ...codexInstallPlan, written: false };
+    }
     const lockEntriesWithTarget = appendTargetEntry(lockEntries, targetPath, targetContent, previousLock);
-    if (anyChanged) {
-        const newRecord = buildLastApply(Object.fromEntries(expected.map((f) => [f.basename, f.content])));
-        const manifestSnapshotJson = JSON.stringify(manifest);
-        newRecord.manifest = {
-            sha256: sha256Hex(manifestSnapshotJson),
-            content: manifestSnapshotJson,
-        };
+    if (anyChanged || recoveredMissingLastApply) {
         const memoryDirSnapshots = collectMemoryDirSnapshots(lockEntries);
-        if (Object.keys(memoryDirSnapshots).length > 0) {
-            newRecord.memoryDirs = memoryDirSnapshots;
-        }
-        writeLastApply(generatedDir, newRecord);
+        writeLastApply(generatedDir, buildMergedLastApplyRecord(expected, lastApply, manifest, memoryDirSnapshots));
     }
     writeLock(lockPath, lockEntriesWithTarget);
     const result = {
@@ -521,10 +617,12 @@ export async function apply(opts = {}) {
         restartHints,
         outcome: "applied",
         lockDrift,
-        written: anyChanged,
+        written: anyChanged || codexInstallResult?.written === true,
         dryRun: false,
         lockPath,
     };
+    if (codexInstallResult)
+        result.codexConfigInstall = codexInstallOutcome(codexInstallResult);
     if (targetPath) {
         result.targetPath = targetPath;
         result.targetWritten = targetWritten;

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

@@ -3,4 +3,11 @@ export interface CodexConfigResult {
     content: string;
     warnings: string[];
 }
+/**
+ * First line of the generated Codex `config.toml`. Exported so callers
+ * that need to detect a harness-generated artifact (e.g. apply.ts's
+ * last-apply baseline recovery) can pin against the same literal as
+ * the emitter, instead of duplicating the string.
+ */
+export declare const CODEX_GENERATED_HEADER_LINE = "# Generated by harness apply --runtime codex.";
 export declare function generateCodexConfig(manifest: Manifest): CodexConfigResult;