@lannguyensi/harness 0.24.0 → 0.25.0

package/CHANGELOG.md

@@ -7,6 +7,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.25.0] - 2026-05-20
+
+**Headline: batch pre-approval for the understanding gate, plus three gate and CLI fixes.** PR #218 makes `harness approve understanding --task` variadic, so a multi-task session (e.g. a CVE sweep across N repos) is pre-approved in one operator action instead of one round-trip per `task_finish`. Three fixes ride along: `harness pause` is a top-level command again (#220, it had been mis-registered as a subcommand of `migrate-home` and dropped from `harness --help`), the `harness approve understanding` session resolver no longer guesses a stale unrelated session from a finished gate cycle (#221), and the Full init template floors agent-preflight at 0.2.0 so secret-detection no longer hard-fails preflight on a normal gitignored `.env` (#219). **Operator action**: none; re-run `npm i -g @lannguyensi/harness` to upgrade.
+
+### Changed
+
+- **FULL_TEMPLATE `git-preflight` hook floors agent-preflight at 0.2.0** (agent-tasks/feffe938). agent-preflight 0.2.0 makes secret detection git-aware and diff-scoped: a gitignored+untracked `.env` holding real credentials (the normal, correct state), a `.md` doc, a non-git directory, or a secret in a tracked file the current branch never touched is reported as a non-blocking `warn` instead of a hard `fail`. Pre-0.2.0 installs hard-fail preflight on that normal state, so the `git-preflight` SessionStart producer (`harness session-start preflight`) never writes a `preflight:` tag and the `preflight-before-*` policies stay closed forever on any repo with a local `.env`. The `min_version` floor on the FULL_TEMPLATE `git-preflight` hook moves `0.1.1` to `0.2.0` (probed by `harness doctor` via `preflight --version`), and the `PROFILE_DEPENDENCIES.full` preflight entry in the `harness init` wizard gains a matching `minVersion: "0.2.0"` so the dependency table surfaces the floor (it previously carried none, the only Full-profile dep without one). The floor is a doctor-warn / wizard-hint, not a forced install: an operator on a stale 0.1.x build still runs, just with the secret-detection footgun and a doctor warning. The `PreflightJson` consumer in `src/cli/session-start/index.ts` is unaffected: it filters checks by `status === "fail" | "error"`, so reclassified `warn` findings drop out cleanly, and the new agent-preflight `path:line` finding format is not parsed. The `init-full-template-pins.test.ts` drift guard moves with the floor.
+
+### Added
+
+- **`harness approve understanding --task` accepts multiple ids: pre-approve a whole task batch in one operator action** (agent-tasks/0dce3880). The understanding gate is task-scoped: the `expire_on_tool_match` PostToolUse hook expires the approval on every `task_finish`, so a multi-task session (e.g. a CVE sweep across N repos) previously needed one `harness approve understanding` round-trip per task. `--task` is now variadic (`--task a b c`, or comma-joined `--task a,b,c`); each id gets its own task-scoped marker written up front. As the agent's active claim cycles through the listed tasks, each `task_start` finds its marker already present, so the operator approves once for the whole batch. The gate stays genuinely task-scoped: the operator's Understanding Report still has to enumerate every task it covers, only the round-trip count collapses. `ApproveUnderstandingOptions` gains `tasks?: string[]` (the back-compat single `task?: string` still works; `tasks` wins when both are set); the result's `taskMarker` field becomes `taskMarkers: TaskMarkerOutcome[]` (empty when no task resolved, one entry per id otherwise). Entries are comma-split, trimmed, and de-duplicated. The CLI prints one `task: ✓ …` line per id plus a batch summary when more than one was written.
+
+### Fixed
+
+- **`harness pause` is registered as a top-level command again** (agent-tasks/8c4825e9). `harness pause` resolved as "unknown command" and was missing from `harness --help`. In `src/cli/index.ts` the `.command("pause")` call was chained directly onto the `migrate-home` command's `.action()`; because Commander's `.command()` returns the newly created subcommand (and `.description()/.option()/.action()` return `this`), that chain registered `pause` as `harness migrate-home pause` rather than as a sibling of the top-level `resume` command. The fix terminates the `migrate-home` chain and starts `pause` as its own `program.command("pause")` statement; the handler and options are unchanged. `migrate-home` itself was never broken (its action still runs when no subcommand is given). New `tests/cli/pause-command-registration.test.ts` drives `buildProgram()` + `run(["--help"])` to assert `pause` is top-level, is not a `migrate-home` subcommand, and appears in the help banner; the pre-existing `pause.test.ts` exercises the `pause()` function directly and so never covered the CLI wiring.
+- **`harness approve understanding` no longer binds a session to a stale, unrelated Understanding Report** (agent-tasks/0dce3880, friction #1). Surfaced 2026-05-20 during a multi-repo CVE sweep: on a fresh session, `harness approve understanding` flipped a two-day-old report from a different investigation to `approved`, because `findLatestReportForSession`'s tolerant fallback adopted any report lacking a `sessionId` field, including one already cycled to `expired` by a prior task. Two complementary fixes: (1) `findLatestReportForSession` gains a `tolerantFallback` option; `harness approve understanding` passes `"uncompleted"`, which makes the sessionId-null fallback skip reports whose `approvalStatus` is a terminal `approved` / `expired` (those belong to a finished cycle and must not be re-adopted) while still accepting a fresh `pending` report. The gate read path (`checkPersistedReport`) and post-tool-use expiry keep the default `"any"` behaviour for back-compat. (2) When `harness approve understanding` flips a report that lacks a `sessionId`, it now stamps the current session id onto the report, so every later lookup strict-matches it and the tolerant fallback can never re-adopt it for a different session. The CLI surfaces this as `; stamped sessionId` on the `report:` line and `persistedReport.sessionIdStamped` in the result. Reports that already carry a `sessionId` are left untouched. The complete fix also wants the standalone `@lannguyensi/understanding-gate` Stop hook to write `sessionId` into reports at capture time; that cross-package change is tracked separately.
+- **`harness approve understanding` no longer guesses a stale, unrelated session from a finished gate cycle** (agent-tasks/56f51f2b). When run without `--session`, without `$CLAUDE_SESSION_ID` / `$CODEX_SESSION_ID`, and without a gate-staged `.pending-approval`, the session-id resolver falls through to tier 5: read the id from the freshest persisted Understanding Report. That tier adopted the newest report regardless of its `approvalStatus`, so an `approved` / `expired` report from a different session days ago (e.g. a stale Codex session) could be picked, the approval marker written for that session, and the live session left gated. Tier 5 now only adopts a `pending` report (a fresh gate cycle no approval has consumed yet), mirroring the `tolerantFallback: "uncompleted"` restriction PR #218 applied to the report-flip path. When every report is already `approved` / `expired`, the command fails loudly with the existing no-session-id error instead of silently approving the wrong session. The residual case (a stale session left a never-approved `pending` report) is now caught by a loud CLI warning: when the id comes from tier 5, `harness approve understanding` prints a `⚠ WARNING` block naming the report file it guessed from and telling the operator to confirm the id against the running agent before trusting the marker. `ApproveUnderstandingResult` gains `newestReportPath`, set only for the `newest-report` source. This is distinct from the report-flip fix above (agent-tasks/0dce3880): that one stopped a stale report being *flipped*, this one stops a stale session id being *resolved*.
+
+## [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.

package/dist/cli/apply/apply.js

@@ -43,7 +43,7 @@ import { EX_NOINPUT, HarnessExitError } from "../exit-codes.js";
 import { loadManifest } from "../loader.js";
 import { GENERATED_DIRNAME, resolveGeneratedDir } from "../../io/generated-dir.js";
 import { resolveHomeDir } from "../../runtime/home-dir.js";
-import { generateCodexConfig } from "./generate-codex-config.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";
@@ -53,6 +53,10 @@ 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);
@@ -225,6 +229,35 @@ 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);
@@ -379,10 +412,18 @@ export async function apply(opts = {}) {
     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,
@@ -493,6 +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,
@@ -556,18 +604,9 @@ export async function apply(opts = {}) {
         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 = {

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

@@ -1 +1 @@
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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;

package/dist/cli/apply/generate-codex-config.js

@@ -28,8 +28,15 @@
 //     the hooks alone are the enforcement.
 import { expandCodexHookMatchPattern } from "../../runtime/tool-name-aliases.js";
 import { buildMemoryRouterHook } from "./generate-settings.js";
+/**
+ * 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 const CODEX_GENERATED_HEADER_LINE = "# Generated by harness apply --runtime codex.";
 const HEADER = [
-    "# Generated by harness apply --runtime codex.",
+    CODEX_GENERATED_HEADER_LINE,
     "# DO NOT EDIT: re-run `harness apply --runtime codex` to regenerate.",
     "#",
     "# Install into ~/.codex/config.toml with:",

package/dist/cli/apply/generate-codex-config.js.map

@@ -1 +1 @@
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package/dist/cli/approve/understanding.d.ts

@@ -17,8 +17,24 @@ export interface ApproveUnderstandingOptions extends LoaderOptions {
      * exists, its content is used as the task id. If absent, no task
      * marker is written — the session marker is the only one (v1
      * back-compat).
+     *
+     * Single-id back-compat field. For pre-approving a batch use `tasks`;
+     * when both are set, `tasks` wins.
      */
     task?: string;
+    /**
+     * Multiple agent-tasks task ids to pre-approve in one operator action
+     * (harness/0dce3880 friction #2). One task-scoped marker is written
+     * per id. As the agent's active claim cycles through the listed
+     * tasks, each `task_start` finds its own marker already present, so a
+     * homogeneous batch (e.g. a CVE sweep across N repos) needs a single
+     * `harness approve understanding --task a b c` instead of one
+     * approval per `task_finish`. The understanding gate stays
+     * task-scoped: the operator's report still has to enumerate every
+     * task it covers; only the round-trip count collapses. Empty / blank
+     * entries are dropped and duplicates de-duplicated.
+     */
+    tasks?: string[];
     /** Override the reports directory (test injection). */
     reportsDir?: string;
     /** Override the harness.generated/ directory (test injection). */
@@ -37,6 +53,19 @@ export interface ApproveUnderstandingOptions extends LoaderOptions {
         reason: string;
     }>;
 }
+/** Outcome of writing one task-scoped approval marker. */
+export type TaskMarkerOutcome = {
+    ok: true;
+    taskId: string;
+    filePath: string;
+    approvedAt: string;
+    source: "flag" | "active-claim";
+} | {
+    ok: false;
+    taskId: string;
+    reason: string;
+    source: "flag" | "active-claim";
+};
 export interface ApproveUnderstandingResult {
     sessionId: string;
     /**
@@ -45,6 +74,14 @@ export interface ApproveUnderstandingResult {
      * which is the moment to sanity-check it against the live session.
      */
     sessionSource: "flag" | "env-claude" | "env-codex" | "pending-approval" | "newest-report";
+    /**
+     * When `sessionSource` is `"newest-report"`, the absolute path of the
+     * persisted report the session id was guessed from. Undefined for
+     * every other source. The CLI names this file in its loud tier-5
+     * "verify this is your live session" warning so the operator can open
+     * it and check before trusting the marker (harness/56f51f2b).
+     */
+    newestReportPath?: string;
     /**
      * Canonical gate-satisfying signal as of agent-tasks/88ca4bb3.
      * `ok: false` means the marker file could not be written (rare:
@@ -61,27 +98,17 @@ export interface ApproveUnderstandingResult {
         reason: string;
     };
     /**
-     * Task-scoped marker write outcome. Present when --task / opts.task
-     * was supplied OR when the active-claim file resolved one
-     * (harness/494fd1e5). Null when no task was resolved through either
-     * surface so a regression cannot silently flip session-only sessions
-     * into task-mode.
+     * Task-scoped marker write outcomes, one entry per resolved task id
+     * (harness/0dce3880). Populated when `--task` / `opts.task` /
+     * `opts.tasks` was supplied OR when the active-claim file resolved an
+     * id (harness/494fd1e5). Empty array when no task was resolved
+     * through any surface, so a regression cannot silently flip
+     * session-only sessions into task-mode.
      *
-     * The `source` field tells the operator which surface fed the id so
+     * The `source` field tells the operator which surface fed each id so
      * a wrong claim file can be spotted before it lands in the marker.
      */
-    taskMarker: {
-        ok: true;
-        taskId: string;
-        filePath: string;
-        approvedAt: string;
-        source: "flag" | "active-claim";
-    } | {
-        ok: false;
-        taskId: string;
-        reason: string;
-        source: "flag" | "active-claim";
-    } | null;
+    taskMarkers: TaskMarkerOutcome[];
     ledger: {
         ok: boolean;
         tag: string;
@@ -92,9 +119,18 @@ export interface ApproveUnderstandingResult {
         filePath: string;
         previousStatus: string | null;
         approvedAt: string;
+        /** True when this approval stamped a missing `sessionId` onto the report. */
+        sessionIdStamped: boolean;
     } | {
         ok: false;
         reason: string;
     };
 }
+/**
+ * Normalise a list of task ids supplied via `opts.tasks` (or the CLI's
+ * variadic `--task`). Each entry is comma-split (so `--task a,b` and
+ * `--task a b` are equivalent), trimmed, blank entries dropped, and the
+ * result de-duplicated while preserving first-seen order.
+ */
+export declare function dedupeTaskIds(raw: string[]): string[];
 export declare function approveUnderstanding(opts?: ApproveUnderstandingOptions): Promise<ApproveUnderstandingResult>;