@lannguyensi/harness 0.35.0 → 0.36.0

package/CHANGELOG.md

@@ -7,6 +7,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.36.0] - 2026-06-16
+
+**Headline: a doctor cleanup mode for rogue ledgers, plus gate-admission and pause-sentinel fixes.** `harness doctor` gains an opt-in `--rm-rogue-ledgers` mode, the read-only Bash classifier re-admits `sort`, `tree`, and `file` behind precise write-flag guards (they were over-blocked), and the runtime-reality gate now honors the pause sentinel like every other gate. Re-run `npm i -g @lannguyensi/harness` to upgrade.
+
+### Added
+
+- **`harness doctor --rm-rogue-ledgers` opt-in cleanup mode** (PR #296). Doctor can now remove rogue evidence ledgers it finds, gated behind an explicit flag so a bare `doctor` run stays read-only.
+
+### Security
+
+- **Validate `sessionId` before joining it into the session-export transcript path** (PR #294). `session-export` joined `sessionId` into the transcript path with no validation; a `rejectMalformedSessionId` guard (rejecting blank values, path separators, and `..`) now runs at the path-construction choke point.
+
+### Fixed
+
+- **Re-admit `sort`, `tree`, and `file` in the read-only Bash classifier behind precise write-flag guards** (PR #292). These commands were over-blocked; they are now admitted unless invoked with a write-producing flag (for example `sort -o`).
+- **Honor the pause sentinel in the runtime-reality gate** (PR #291). The runtime-reality checker now respects the pause sentinel like every other gate instead of firing while the harness is paused.
+
+### Changed
+
+- **Dedupe `rejectMalformedSessionId` to the shared runtime helper** (PR #295) and **extract a shared `resolveApprovalSessionId`** (PR #293, discovery M5). Internal refactors consolidating session-id handling, with no behavior change.
+- **Remove em dashes from prose** per the org style rule (PR #290).
+
 ## [0.35.0] - 2026-06-14
 
 **Headline: the Tier-1 discovery follow-up.** The five HIGH findings from the 2026-06-10 discovery audit are fixed: a defense-in-depth gap in the approval-marker path, the long-standing `harness add` whole-manifest footgun, a solution-acceptance verdict-dir mismatch, a policy-degradation footgun that `apply` did not catch, and an integration suite that never ran in CI. **Operator action**: `harness apply` now refuses a manifest that declares `policies:` without wiring grounding-mcp under `tools.mcp` (previously it applied and the policies silently degraded to warn-mode at runtime); wire grounding-mcp or remove the policies. Re-run `npm i -g @lannguyensi/harness` to upgrade.

package/dist/cli/approve/branch-protection.js

@@ -17,7 +17,8 @@
 // a warning, never a hard failure: the marker is what unblocks the gate.
 import { ACK_TAG_PREFIX, writeBranchProtectionMarker, } from "../../policy-packs/builtin/branch-protection-runtime.js";
 import { addLedgerFact } from "../../runtime/ledger-add.js";
-import { readPendingApproval, resolveGeneratedDir, } from "../../runtime/pending-approval.js";
+import { resolveGeneratedDir } from "../../runtime/pending-approval.js";
+import { resolveApprovalSessionId } from "../../runtime/session-id.js";
 import { EX_FAIL, HarnessExitError } from "../exit-codes.js";
 import { loadManifest, resolvePaths } from "../loader.js";
 const DEFAULT_APPROVED_BY = "harness-approve-cli";
@@ -70,34 +71,20 @@ export async function approveBranchProtection(opts = {}) {
             ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
             manifestPath: resolvePaths(opts).base,
         });
-    let sessionId = "";
-    let sessionSource = "flag";
-    if (typeof opts.session === "string" && opts.session.length > 0) {
-        sessionId = opts.session;
-        sessionSource = "flag";
-    }
-    else if (typeof process.env.CLAUDE_CODE_SESSION_ID === "string" &&
-        process.env.CLAUDE_CODE_SESSION_ID.length > 0) {
-        sessionId = process.env.CLAUDE_CODE_SESSION_ID;
-        sessionSource = "env-claude-code";
-    }
-    else if (typeof process.env.CLAUDE_SESSION_ID === "string" &&
-        process.env.CLAUDE_SESSION_ID.length > 0) {
-        sessionId = process.env.CLAUDE_SESSION_ID;
-        sessionSource = "env-claude";
-    }
-    else if (typeof process.env.CODEX_SESSION_ID === "string" &&
-        process.env.CODEX_SESSION_ID.length > 0) {
-        sessionId = process.env.CODEX_SESSION_ID;
-        sessionSource = "env-codex";
-    }
-    else {
-        const staged = readPendingApproval(generatedDir);
-        if (staged !== null) {
-            sessionId = staged;
-            sessionSource = "pending-approval";
-        }
-    }
+    // Session id precedence mirrors `harness approve risk` tiers 1-5:
+    // explicit --session, then $CLAUDE_CODE_SESSION_ID (canonical Claude Code
+    // var), then $CLAUDE_SESSION_ID (legacy), then $CODEX_SESSION_ID, then the
+    // .pending-approval file staged by the gate hook or preflight. No
+    // persisted-report tier: the branch-protection gate produces no persisted
+    // reports.
+    const { sessionId, sessionSource: rawSessionSource } = resolveApprovalSessionId({
+        session: opts.session,
+        generatedDir,
+    });
+    // Cast is safe: no newestReportFallback passed, so "newest-report" is
+    // unreachable at runtime. The wider return type of resolveApprovalSessionId
+    // requires the cast for TypeScript.
+    const sessionSource = rawSessionSource;
     if (sessionId === "") {
         throw new HarnessExitError([
             "no session id available. Pass --session <id>, or set one of",

package/dist/cli/approve/branch-protection.js.map

@@ -1 +1 @@
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package/dist/cli/approve/risk.js

@@ -14,7 +14,8 @@
 // (docs/risk-gate.md "Decision model") specifies. `agent-grounding`
 // needs no change: it already stores arbitrary tags through `ledger_add`.
 import { addLedgerFact } from "../../runtime/ledger-add.js";
-import { readPendingApproval, resolveGeneratedDir, } from "../../runtime/pending-approval.js";
+import { resolveGeneratedDir } from "../../runtime/pending-approval.js";
+import { resolveApprovalSessionId } from "../../runtime/session-id.js";
 import { EX_FAIL, EX_USAGE, HarnessExitError } from "../exit-codes.js";
 import { loadManifest, resolvePaths } from "../loader.js";
 const RISK_APPROVED_PREFIX = "risk-approved";
@@ -124,38 +125,19 @@ export async function approveRisk(opts = {}) {
             ...(opts.homeDir !== undefined ? { homeDir: opts.homeDir } : {}),
             manifestPath: resolvePaths(opts).base,
         });
-    let sessionId = "";
-    let sessionSource = "flag";
-    if (typeof opts.session === "string" && opts.session.length > 0) {
-        sessionId = opts.session;
-        sessionSource = "flag";
-    }
-    else if (typeof process.env.CLAUDE_CODE_SESSION_ID === "string" &&
-        process.env.CLAUDE_CODE_SESSION_ID.length > 0) {
-        // Canonical: the var Claude Code actually exports into the agent
-        // shell. Read before the legacy $CLAUDE_SESSION_ID so an operator
-        // who has both set (e.g. a manual export plus the runtime export)
-        // gets the runtime's id, not whatever they typed by hand.
-        sessionId = process.env.CLAUDE_CODE_SESSION_ID;
-        sessionSource = "env-claude-code";
-    }
-    else if (typeof process.env.CLAUDE_SESSION_ID === "string" &&
-        process.env.CLAUDE_SESSION_ID.length > 0) {
-        sessionId = process.env.CLAUDE_SESSION_ID;
-        sessionSource = "env-claude";
-    }
-    else if (typeof process.env.CODEX_SESSION_ID === "string" &&
-        process.env.CODEX_SESSION_ID.length > 0) {
-        sessionId = process.env.CODEX_SESSION_ID;
-        sessionSource = "env-codex";
-    }
-    else {
-        const staged = readPendingApproval(generatedDir);
-        if (staged !== null) {
-            sessionId = staged;
-            sessionSource = "pending-approval";
-        }
-    }
+    // Session id precedence mirrors `harness approve understanding` tiers 1-5:
+    // explicit --session, then $CLAUDE_CODE_SESSION_ID (canonical Claude Code
+    // var), then $CLAUDE_SESSION_ID (legacy), then $CODEX_SESSION_ID, then the
+    // .pending-approval file staged by the gate hook or preflight. No
+    // persisted-report tier: the Risk Gate produces no persisted reports.
+    const { sessionId, sessionSource: rawSessionSource } = resolveApprovalSessionId({
+        session: opts.session,
+        generatedDir,
+    });
+    // Cast is safe: no newestReportFallback passed, so "newest-report" is
+    // unreachable at runtime. The wider return type of resolveApprovalSessionId
+    // requires the cast for TypeScript.
+    const sessionSource = rawSessionSource;
     if (sessionId === "") {
         throw new HarnessExitError([
             "no session id available. Pass --session <id>, or set one of",

package/dist/cli/approve/risk.js.map

@@ -1 +1 @@
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package/dist/cli/approve/understanding.js

@@ -19,7 +19,8 @@ import * as path from "node:path";
 import { atomicWriteFile } from "../../io/atomic-write.js";
 import { approvedLedgerTagFor, defaultReportsDir, listPersistedReports, readActiveClaim, selectReportForSession, TOLERANT_FALLBACK_MAX_AGE_MS, writeApprovalMarker, writeTaskApprovalMarker, } from "../../policy-packs/builtin/understanding-before-execution-runtime.js";
 import { addLedgerFact } from "../../runtime/ledger-add.js";
-import { clearPendingApproval, readPendingApproval, resolveGeneratedDir, } from "../../runtime/pending-approval.js";
+import { clearPendingApproval, resolveGeneratedDir, } from "../../runtime/pending-approval.js";
+import { resolveApprovalSessionId } from "../../runtime/session-id.js";
 import { EX_FAIL, HarnessExitError } from "../exit-codes.js";
 import { loadManifest, resolvePaths } from "../loader.js";
 /**
@@ -275,56 +276,33 @@ export async function approveUnderstanding(opts = {}) {
     // HARNESS_ALLOW_REAL_GENERATED_DIR loader guard.
     const reportsDir = opts.reportsDir ??
         defaultReportsDir(path.dirname(resolvePaths(opts).base));
-    let sessionId = "";
-    let sessionSource = "flag";
-    let newestReportPath;
-    if (typeof opts.session === "string" && opts.session.length > 0) {
-        sessionId = opts.session;
-        sessionSource = "flag";
-    }
-    else if (typeof process.env.CLAUDE_CODE_SESSION_ID === "string" &&
-        process.env.CLAUDE_CODE_SESSION_ID.length > 0) {
-        sessionId = process.env.CLAUDE_CODE_SESSION_ID;
-        sessionSource = "env-claude-code";
-    }
-    else if (typeof process.env.CLAUDE_SESSION_ID === "string" &&
-        process.env.CLAUDE_SESSION_ID.length > 0) {
-        sessionId = process.env.CLAUDE_SESSION_ID;
-        sessionSource = "env-claude";
-    }
-    else if (typeof process.env.CODEX_SESSION_ID === "string" &&
-        process.env.CODEX_SESSION_ID.length > 0) {
-        sessionId = process.env.CODEX_SESSION_ID;
-        sessionSource = "env-codex";
-    }
-    else {
-        const staged = readPendingApproval(generatedDir);
-        if (staged !== null) {
-            sessionId = staged;
-            sessionSource = "pending-approval";
-        }
-        else {
-            // Tier 5: guess the session from the freshest persisted report.
-            // Restricted to `pending` reports. An `approved` / `expired`
-            // report belongs to a finished gate cycle (often a different
-            // session days ago); adopting its sessionId silently approves an
-            // unrelated session while the live one stays gated
-            // (harness/56f51f2b). A `pending` report is one the Stop hook
-            // just produced that no approval has consumed yet, so it is far
-            // more likely to be the current session's. This mirrors the
-            // `tolerantFallback: "uncompleted"` restriction PR #218 applied
-            // to the report-flip path below. The residual case — a stale
-            // session left a never-approved `pending` report — is caught by
-            // the loud tier-5 warning the CLI prints, which names the report
-            // file so the operator can verify before trusting the marker.
+    const resolved = resolveApprovalSessionId({
+        session: opts.session,
+        generatedDir,
+        // Tier 6: guess the session from the freshest persisted report.
+        // Restricted to `pending` reports. An `approved` / `expired`
+        // report belongs to a finished gate cycle (often a different
+        // session days ago); adopting its sessionId silently approves an
+        // unrelated session while the live one stays gated
+        // (harness/56f51f2b). A `pending` report is one the Stop hook
+        // just produced that no approval has consumed yet, so it is far
+        // more likely to be the current session's. This mirrors the
+        // `tolerantFallback: "uncompleted"` restriction PR #218 applied
+        // to the report-flip path below. The residual case — a stale
+        // session left a never-approved `pending` report — is caught by
+        // the loud newest-report warning the CLI prints, which names the report
+        // file so the operator can verify before trusting the marker.
+        newestReportFallback: () => {
             const newest = listPersistedReports(reportsDir).find((r) => r.sessionId !== null && r.approvalStatus === "pending");
             if (newest && newest.sessionId !== null) {
-                sessionId = newest.sessionId;
-                sessionSource = "newest-report";
-                newestReportPath = newest.filePath;
+                return { sessionId: newest.sessionId, filePath: newest.filePath };
             }
-        }
-    }
+            return null;
+        },
+    });
+    const sessionId = resolved.sessionId;
+    const sessionSource = resolved.sessionSource;
+    const newestReportPath = resolved.newestReportPath;
     if (sessionId === "") {
         // Reaching here means: no --session flag, no $CLAUDE_CODE_SESSION_ID
         // / $CLAUDE_SESSION_ID / $CODEX_SESSION_ID env, no staged

package/dist/cli/approve/understanding.js.map

@@ -1 +1 @@
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package/dist/cli/doctor/rogue-ledger.d.ts

@@ -23,3 +23,31 @@ export interface RogueLedgerScanOptions {
  * results (by realpath) sorted by path for stable rendering.
  */
 export declare function scanForRogueLedgers(opts: RogueLedgerScanOptions): RogueLedgerDb[];
+export interface DeleteRogueLedgersOptions {
+    /**
+     * When true, skip per-hit confirmation prompts and delete immediately.
+     * Maps to `harness doctor --rm-rogue-ledgers --yes`.
+     */
+    yes?: boolean;
+    /**
+     * Test injection: called per hit with the rogueDir path; returns true to
+     * confirm deletion, false to skip. When omitted and `yes` is false,
+     * production code prompts via readline on stdin.
+     * Same knob pattern as `mcpProbe` / `fsInterface` elsewhere in doctor.
+     */
+    promptFn?: (rogueDir: string) => Promise<boolean>;
+}
+export interface DeleteRogueLedgersResult {
+    /** Hits that were confirmed and whose rogueDir was removed. */
+    deleted: RogueLedgerDb[];
+    /** Hits that were skipped (operator declined or safety check failed). */
+    skipped: RogueLedgerDb[];
+}
+/**
+ * Delete confirmed rogue ledger directories.
+ *
+ * Safety invariant: only deletes `hit.rogueDir` (the literal-tilde `~`
+ * directory), never its parent. Any hit whose rogueDir basename is not
+ * exactly `~` is silently skipped as a belt-and-suspenders guard.
+ */
+export declare function deleteRogueLedgers(hits: RogueLedgerDb[], opts?: DeleteRogueLedgersOptions): Promise<DeleteRogueLedgersResult>;

package/dist/cli/doctor/rogue-ledger.js

@@ -17,6 +17,7 @@
 // recursion past one level: we are not a generic disk-cleanup tool.
 import * as fs from "node:fs";
 import * as path from "node:path";
+import * as readline from "node:readline/promises";
 const ROGUE_DIRNAME = "~";
 const LEDGER_RELPATH = path.join(".evidence-ledger", "ledger.db");
 function hasRogueLedgerUnder(parent, fsi) {
@@ -103,4 +104,50 @@ export function scanForRogueLedgers(opts) {
     out.sort((a, b) => a.path.localeCompare(b.path));
     return out;
 }
+/**
+ * Delete confirmed rogue ledger directories.
+ *
+ * Safety invariant: only deletes `hit.rogueDir` (the literal-tilde `~`
+ * directory), never its parent. Any hit whose rogueDir basename is not
+ * exactly `~` is silently skipped as a belt-and-suspenders guard.
+ */
+export async function deleteRogueLedgers(hits, opts = {}) {
+    const deleted = [];
+    const skipped = [];
+    for (const hit of hits) {
+        // Safety: only ever remove a directory whose basename is the literal `~`.
+        if (path.basename(hit.rogueDir) !== "~") {
+            skipped.push(hit);
+            continue;
+        }
+        let confirmed;
+        if (opts.yes) {
+            confirmed = true;
+        }
+        else if (opts.promptFn) {
+            confirmed = await opts.promptFn(hit.rogueDir);
+        }
+        else {
+            confirmed = await defaultDeletePrompt(hit.rogueDir);
+        }
+        if (confirmed) {
+            fs.rmSync(hit.rogueDir, { recursive: true, force: true });
+            deleted.push(hit);
+        }
+        else {
+            skipped.push(hit);
+        }
+    }
+    return { deleted, skipped };
+}
+async function defaultDeletePrompt(rogueDir) {
+    const rl = readline.createInterface({ input: process.stdin, output: process.stderr });
+    try {
+        const answer = await rl.question(`Delete rogue directory ${rogueDir}? (y/N) `);
+        return answer.trim().toLowerCase() === "y";
+    }
+    finally {
+        rl.close();
+    }
+}
 //# sourceMappingURL=rogue-ledger.js.map

package/dist/cli/doctor/rogue-ledger.js.map

@@ -1 +1 @@
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package/dist/cli/index.d.ts

@@ -1,8 +1,17 @@
 import { Command } from "commander";
+import { type RogueLedgerScanOptions } from "./doctor/rogue-ledger.js";
 export interface RunOptions {
     argv?: string[];
     stdout?: (s: string) => void;
     stderr?: (s: string) => void;
+    /**
+     * Test-injection knob for `harness doctor --rm-rogue-ledgers`. When set,
+     * both the initial scan (forwarded to `doctor()`) and the post-deletion
+     * re-scan use these options instead of the runtime `os.homedir()` /
+     * `process.cwd()` defaults. This makes the re-scan fully hermetic in unit
+     * tests without spawning real filesystem side-effects.
+     */
+    rogueLedgerScanOptions?: Partial<RogueLedgerScanOptions>;
 }
 export declare function buildProgram(opts?: RunOptions): Command;
 export declare function run(opts?: RunOptions): Promise<number>;

package/dist/cli/index.js

@@ -1,5 +1,6 @@
 import { spawnSync } from "node:child_process";
 import * as fs from "node:fs";
+import * as os from "node:os";
 import * as path from "node:path";
 import { Command } from "commander";
 // Production version probe for `harness doctor`: synchronous --version
@@ -43,6 +44,7 @@ import { diffSinceApply } from "./diff/since-apply.js";
 import { exportManifest } from "./export.js";
 import { doctor, isDoctorTarget, KNOWN_DOCTOR_TARGETS } from "./doctor/index.js";
 import { format as formatDoctor } from "./doctor/format.js";
+import { deleteRogueLedgers, scanForRogueLedgers, } from "./doctor/rogue-ledger.js";
 import { EX_FAIL, EX_USAGE, HarnessExitError } from "./exit-codes.js";
 import { explain } from "./explain.js";
 import { explainAction } from "./explain-action.js";
@@ -165,7 +167,9 @@ export function buildProgram(opts = {}) {
         .option("--project <name>", "apply per-project overrides for this project name")
         .option("--shallow", "skip MCP probes (CLI --version probes still run); report manifest-reference state only")
         .option("--target <runtime>", `additionally evaluate the harness-side adapter health for a runtime (allowed: ${KNOWN_DOCTOR_TARGETS.join(", ")})`)
-        .option("--json", "emit a structured JSON DoctorReport instead of prose")
+        .option("--json", "emit a structured JSON DoctorReport instead of prose (--rm-rogue-ledgers is ignored with --json)")
+        .option("--rm-rogue-ledgers", "after reporting, delete each rogue evidence-ledger directory found (prompts per hit; combine with --yes to skip prompts)")
+        .option("--yes", "with --rm-rogue-ledgers, skip per-hit confirmation prompts")
         .action(async (options) => {
         let target;
         if (options.target !== undefined) {
@@ -181,12 +185,41 @@ export function buildProgram(opts = {}) {
             shallow: options.shallow,
             versionProbe: defaultVersionProbe,
             ...(target !== undefined ? { target } : {}),
+            ...(opts.rogueLedgerScanOptions !== undefined
+                ? { rogueLedgerScanOptions: opts.rogueLedgerScanOptions }
+                : {}),
         });
         if (options.json) {
             stdout(`${JSON.stringify(report, null, 2)}\n`);
             return;
         }
         stdout(formatDoctor(report));
+        if (!options.rmRogueLedgers)
+            return;
+        const hits = report.rogueLedgerDbs;
+        if (hits.length === 0) {
+            stdout("no rogue evidence-ledger DBs found; nothing to delete\n");
+            return;
+        }
+        const result = await deleteRogueLedgers(hits, { yes: options.yes });
+        for (const hit of result.deleted) {
+            stdout(`deleted: ${hit.rogueDir}\n`);
+        }
+        for (const hit of result.skipped) {
+            stdout(`skipped: ${hit.rogueDir}\n`);
+        }
+        // Re-scan and print clean delta so the operator can confirm the
+        // on-disk state after deletion. Uses the same scan options as the
+        // initial scan (injectable via RunOptions.rogueLedgerScanOptions for
+        // tests; production falls back to os.homedir() / process.cwd()).
+        const afterScan = scanForRogueLedgers({
+            homeDir: opts.rogueLedgerScanOptions?.homeDir ?? os.homedir(),
+            cwd: opts.rogueLedgerScanOptions?.cwd ?? process.cwd(),
+            ...(opts.rogueLedgerScanOptions?.fsInterface !== undefined
+                ? { fsInterface: opts.rogueLedgerScanOptions.fsInterface }
+                : {}),
+        });
+        stdout(`rogue evidence-ledger DBs remaining: ${afterScan.length}\n`);
     });
     program
         .command("list <category>")