@lannguyensi/harness 0.64.0 → 1.0.0

package/dist/cli/diff/index.js

@@ -1,9 +1,9 @@
 import * as fs from "node:fs";
 import { parse as parseYaml } from "yaml";
-import { OverrideMergeError, applyLayers } from "../../overrides/merge.js";
+import { OverrideMergeError } from "../../overrides/merge.js";
+import { mergeLayersStrippingRemovedPaths } from "../../overrides/merge-layers.js";
 import { ManifestParseError, parseManifest } from "../../schema/index.js";
 import { EX_NOINPUT, EX_USAGE, HarnessExitError } from "../exit-codes.js";
-import { withDerivedPolicies } from "../../runtime/workflow-policies.js";
 import { loadManifest, resolvePaths } from "../loader.js";
 import { diffManifests, formatDiff } from "./engine.js";
 import { locateGitContext, readFileAtRefOrNull, readManifestAtRef, repoRelativePath, } from "./git.js";
@@ -17,27 +17,12 @@ function parseRefYaml(raw, label) {
 }
 /**
  * Parse the ref-side manifest into the SAME view the working side gets
- * from `loadManifest`: hand-authored policies plus the `workflows[]`-
- * derived merge-gate pair (review round 3, 99f47307 Slice 1). Before
- * this the ref side was `parseManifest` alone, so an unchanged manifest
- * with a qualifying workflow diffed as `+ policies[workflow:<name>:
- * review-before-merge(-bash)]` on every run. Derived on both sides (not
- * stripped on both) because `harness diff` is an effective-config diff,
- * the same reason override layers are merged on both sides: flipping a
- * review step from `spawn: optional` to `required` since the ref changes
- * what `policy intercept` enforces, and the diff should say so.
- *
- * Residual (F4, review round 3, 99f47307 Slice 1): both sides derive with
- * the CURRENT (working-tree) harness version's derivation logic, since
- * this function runs in-process rather than at the ref's own checked-out
- * code. A change to the derivation logic itself between harness releases
- * therefore never shows up as a diff, even when the ref predates that
- * change: `diff --since` compares manifest content across versions, not
- * derivation behavior across versions.
+ * from `loadManifest`: removed keys are stripped the same way, so an
+ * unchanged manifest never diffs as a change.
  */
 function parseRefSchema(parsed) {
     try {
-        return withDerivedPolicies(parseManifest(parsed));
+        return parseManifest(parsed);
     }
     catch (err) {
         if (err instanceof ManifestParseError) {
@@ -71,7 +56,9 @@ function parseRefSchema(parsed) {
  * consciously out of scope here.
  */
 function buildRefManifest(ctx, since, refRaw, layerPaths, warnings) {
-    const refLayerRaws = [];
+    // Label each ref-side layer with its file path, so a layer root that is
+    // not a mapping names the file in the error, as on the working side.
+    const refLayers = [];
     for (const layerPath of layerPaths) {
         const rel = repoRelativePath(ctx, layerPath);
         if (rel === null) {
@@ -87,19 +74,21 @@ function buildRefManifest(ctx, since, refRaw, layerPaths, warnings) {
                 // unreadable between that existsSync and this read.
                 throw new HarnessExitError(`override layer could not be read: ${layerPath}: ${err.message}`, EX_NOINPUT);
             }
-            refLayerRaws.push(parseRefYaml(raw, `override layer ${layerPath}`));
+            refLayers.push({ raw: parseRefYaml(raw, `override layer ${layerPath}`), label: `override layer ${layerPath}` });
             continue;
         }
         const atRef = readFileAtRefOrNull(ctx, since, rel);
         if (atRef === null)
             continue; // layer added since <ref>: a real change
-        refLayerRaws.push(parseRefYaml(atRef, `override layer ${rel} at git ref "${since}"`));
+        refLayers.push({ raw: parseRefYaml(atRef, `override layer ${rel} at git ref "${since}"`), label: `override layer ${layerPath}` });
     }
     const baseRaw = parseRefYaml(refRaw, "manifest at git ref");
-    if (refLayerRaws.length === 0)
+    if (refLayers.length === 0)
         return parseRefSchema(baseRaw);
     try {
-        return parseRefSchema(applyLayers(baseRaw, ...refLayerRaws));
+        // Removed keys are stripped from the ref-time base and layers before the
+        // merge, as the working side does (the ref-side warnings are not reported).
+        return parseRefSchema(mergeLayersStrippingRemovedPaths(baseRaw, refLayers).merged);
     }
     catch (err) {
         // A shape conflict between the REF-time base and a layer is a new

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

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package/dist/cli/doctor/claude-mcp.d.ts

@@ -35,8 +35,7 @@ export interface ClaudeMcpRegistrationSection {
     /**
      * Roll-up warnings (list unavailable for a reason other than "CLI not
      * installed", dead settings.json block). Each rolls into
-     * `warningCount`, mirroring `GroundingSection.warnings` /
-     * `RiskGateSection.warnings`.
+     * `warningCount`, mirroring `GroundingSection.warnings`.
      */
     warnings: string[];
 }
@@ -52,18 +51,6 @@ export interface BuildClaudeMcpRegistrationOptions {
     shallow?: boolean;
     /** Test-injection knob; production omits this and the real `claude` CLI is spawned. */
     claudeMcpExec?: ClaudeMcpExec;
-    /**
-     * The `harness.generated/` directory for the manifest in use (review
-     * round H1, Finding 2), threaded to `buildDesiredMcpServers` so the
-     * desired projection — and therefore the "not registered" `claude mcp
-     * add-json ...` hint — carries `SOLUTION_VERDICT_SIGNING_KEY` exactly
-     * like `apply`/`init --interactive`/opencode's config generator project
-     * it. The caller (doctor/index.ts) resolves this the same way apply.ts
-     * and interactive.ts do: `resolveGeneratedDir({homeDir, manifestPath})`.
-     * Omitted -> no signing-key projection, mirroring
-     * `BuildDesiredMcpServersOptions.generatedDir`'s own no-safe-default rule.
-     */
-    generatedDir?: string;
 }
 /**
  * Resolve the settings.json path the dead-block check reads. Mirrors the
@@ -72,11 +59,9 @@ export interface BuildClaudeMcpRegistrationOptions {
  * (`$CLAUDE_CONFIG_DIR/settings.json`), otherwise it is
  * `~/.claude/settings.json` under the operator home.
  *
- * Exported (ADR docs/decisions/2026-08-27-ug-auto-mode-approval.md slice
- * 1, agent-tasks 74b4b17d): `settings-drift.ts` reuses the same
- * resolution for the user-scope file in its `permissions.defaultMode` /
- * hook-roster drift check, so there is one authority for "where is the
- * user settings.json" instead of a second, possibly-diverging copy.
+ * Exported (agent-tasks 74b4b17d): this is the single authority for
+ * "where is the user settings.json", so other readers share this
+ * resolution instead of keeping a second, possibly-diverging copy.
  */
 export declare function resolveSettingsPath(home: string, env: NodeJS.ProcessEnv): string;
 export declare function buildClaudeMcpRegistration(manifest: Manifest, opts: BuildClaudeMcpRegistrationOptions): Promise<ClaudeMcpRegistrationSection>;

package/dist/cli/doctor/claude-mcp.js

@@ -6,8 +6,9 @@
 // module header for the full story and the verified CLI contract.
 //
 // Runtime gating (per the task spec): doctor has no clean per-runtime
-// concept to further scope this check on — `KNOWN_DOCTOR_TARGETS` (see
-// `types.ts`) only carries `codex` today, with no `claude-code` entry.
+// concept to further scope this check on: `KNOWN_DOCTOR_TARGETS` (see
+// `types.ts`) carries `codex` and `opencode` today, with no
+// `claude-code` entry.
 // The section therefore gates purely on `tools.mcp[]` being non-empty and
 // documents the "assumes Claude Code is the effective runtime" caveat in
 // its own rendered output (see `format.ts`'s `formatClaudeMcpSection`)
@@ -17,7 +18,7 @@
 // `--shallow` and at least one manifest MCP server is enabled (nothing to
 // verify otherwise). Callers that don't want the real CLI touched (every
 // test in this repo) inject `claudeMcpExec`, mirroring the
-// `npmBinExec`/`gitIgnoreProbe` injectable-exec convention already used
+// `npmBinExec` injectable-exec convention already used
 // elsewhere in this directory.
 import * as fs from "node:fs";
 import * as path from "node:path";
@@ -31,11 +32,9 @@ import { DEFAULT_OWNED_MCP_SERVERS } from "../uninstall/index.js";
  * (`$CLAUDE_CONFIG_DIR/settings.json`), otherwise it is
  * `~/.claude/settings.json` under the operator home.
  *
- * Exported (ADR docs/decisions/2026-08-27-ug-auto-mode-approval.md slice
- * 1, agent-tasks 74b4b17d): `settings-drift.ts` reuses the same
- * resolution for the user-scope file in its `permissions.defaultMode` /
- * hook-roster drift check, so there is one authority for "where is the
- * user settings.json" instead of a second, possibly-diverging copy.
+ * Exported (agent-tasks 74b4b17d): this is the single authority for
+ * "where is the user settings.json", so other readers share this
+ * resolution instead of keeping a second, possibly-diverging copy.
  */
 export function resolveSettingsPath(home, env) {
     const configDir = env["CLAUDE_CONFIG_DIR"];
@@ -104,11 +103,9 @@ export async function buildClaudeMcpRegistration(manifest, opts) {
     // apply/init pass no homeDir and fall back to os.homedir(); the two only
     // diverge when doctor is pointed at a DIFFERENT home than the one the
     // process runs as, in which case doctor's hint is the correct one for
-    // that home. For the signing key the shared signingKeyEnvValue resolves
-    // non-absolute generatedDir inputs the same way at every call site.
+    // that home.
     const { mcp: desired } = buildDesiredMcpServers(manifest, {
         homeDir: opts.home,
-        generatedDir: opts.generatedDir,
     });
     const desiredNames = Object.keys(desired).sort();
     const warnings = [];
@@ -148,8 +145,9 @@ export async function buildClaudeMcpRegistration(manifest, opts) {
                     entries.push({
                         name,
                         status: "error",
-                        message: "not registered with the claude CLI — run `harness init --interactive` or " +
-                            `\`claude mcp add-json --scope user ${name} ${posixSingleQuote(JSON.stringify(desired[name]))}\``,
+                        message: "not registered with the claude CLI; run " +
+                            `\`claude mcp add-json --scope user ${name} ${posixSingleQuote(JSON.stringify(desired[name]))}\`` +
+                            " (`harness init --interactive` also registers, but on an existing install it offers to overwrite harness.yaml)",
                     });
                     continue;
                 }
@@ -171,15 +169,6 @@ export async function buildClaudeMcpRegistration(manifest, opts) {
                             message: found.statusText || "Needs authentication",
                         });
                         break;
-                    default:
-                        // Defensive: markerToStatus in io/claude-mcp.ts only returns
-                        // "unknown" for a marker glyph the verified CLI contract has
-                        // never produced. Warn rather than silently drop it.
-                        entries.push({
-                            name,
-                            status: "warn",
-                            message: `unrecognised claude mcp list status (${found.statusText || "unknown"})`,
-                        });
                 }
             }
         }

package/dist/cli/doctor/claude-mcp.js.map

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

@@ -1,4 +1,4 @@
-import type { Manifest } from "../../schema/index.js";
+import type { Hook, Manifest } from "../../schema/index.js";
 import { countStatusDiagnostics, type DoctorCheckStatus } from "./target-checks.js";
 export { countStatusDiagnostics };
 export type CodexCheckStatus = DoctorCheckStatus;
@@ -6,6 +6,11 @@ export interface CodexCheckEntry {
     name: string;
     status: CodexCheckStatus;
     message: string;
+    /**
+     * The finding is already tallied by another doctor section (the manifest
+     * warnings), so the target tally skips it. It still renders at its status.
+     */
+    countedElsewhere?: boolean;
 }
 export interface CodexTargetReport {
     target: "codex";
@@ -14,25 +19,12 @@ export interface CodexTargetReport {
 export interface RunCodexCheckOptions {
     /** Manifest directory; the codex config is at <dir>/harness.generated/codex/config.toml. */
     manifestDir: string;
-    /**
-     * Pre-task-4f4a1178: working directory used to resolve the persisted-
-     * report path. Retained for compat but ignored — the report dir is
-     * now resolved via `defaultReportsDir(manifestDir)` so the doctor's
-     * answer matches what apply bakes into the hook commands.
-     */
-    cwd?: string;
     /** Override for $PATH lookup (test injection). */
     pathEnv?: string;
     /** Override for path existence + executable check (test injection). */
     isExecutable?: (p: string) => boolean;
     /** Override for the `harness` binary location (test injection). */
     harnessBinary?: string;
-    /**
-     * Override for the `harness --version` probe. Returns null when the
-     * probe could not run (binary missing, spawn error, non-zero exit).
-     * Returns the trimmed stdout otherwise. Test injection only.
-     */
-    versionProbe?: (binary: string) => string | null;
 }
 /**
  * Resolve `binary` against `pathEnv`: absolute paths resolve to themselves
@@ -42,6 +34,12 @@ export interface RunCodexCheckOptions {
  * near-identical copy (the check:duplication fitness function flags that).
  */
 export declare function findOnPath(binary: string, pathEnv: string, isExecutable: (p: string) => boolean): string | null;
+/**
+ * `expansionHooks` are the hooks the codex pack expansion contributes; they
+ * default to the real expansion and are a parameter so a test can feed one
+ * that calls a removed verb.
+ */
+export declare function checkHookCommands(manifest: Manifest, pathEnv: string, isExecutable: (p: string) => boolean, expansionHooks?: Hook[]): CodexCheckEntry[];
 export declare function runCodexTargetChecks(manifest: Manifest, opts: RunCodexCheckOptions): CodexTargetReport;
 export declare function countCodexDiagnostics(report: CodexTargetReport): {
     errorCount: number;

package/dist/cli/doctor/codex.js

@@ -1,22 +1,20 @@
 // Phase 6 #6 follow-up — `harness doctor --target codex` checks.
 //
 // Validates the wiring shipped in Phase 6 #6: the harness CLI itself is
-// reachable (so the `harness pack hook codex-*` subcommands resolve),
+// reachable (so hook commands that invoke `harness` resolve),
 // the harness-generated `harness.generated/codex/config.toml` exists,
 // every contributed `[[hooks.*]]` stanza references a command that
-// resolves on PATH, and the persisted-report directory is writable.
+// resolves on PATH.
 //
 // The checks here intentionally do NOT exercise the actual Codex CLI
 // binary — that is a Codex-runtime concern, out of harness's scope.
 // What this module guarantees is "the harness side of the integration
 // is wired correctly"; whether Codex itself reads the emitted TOML is
 // up to the operator's `~/.codex/config.toml` setup.
-import { spawnSync } from "node:child_process";
 import * as fs from "node:fs";
 import * as path from "node:path";
-import { defaultReportsDir } from "../../policy-packs/builtin/understanding-before-execution-runtime.js";
 import { expandPolicyPacks } from "../../policy-packs/index.js";
-import { VERSION as HARNESS_VERSION } from "../../version.js";
+import { invokesRemovedCommand, removedCommandMessage } from "../../schema/removed-keys.js";
 import { countStatusDiagnostics } from "./target-checks.js";
 // LOW-F5 (batch18 fix-round, task f34eb233 review): re-exported for
 // import-path compatibility -- see target-checks.ts's header for why
@@ -90,7 +88,7 @@ function resolveHarnessBinary(opts, override) {
             entry: {
                 name: "harness binary",
                 status: "error",
-                message: "`harness` not found on PATH; the codex-* subcommands cannot be invoked. Install harness globally or expose its bin via PATH.",
+                message: "`harness` not found on PATH; hook commands that invoke `harness` cannot run. Install harness globally or expose its bin via PATH.",
             },
             resolved: null,
         };
@@ -104,86 +102,6 @@ function resolveHarnessBinary(opts, override) {
         resolved,
     };
 }
-// Phase 6 #6 ships in 0.7.0 (the version this module is shipped from).
-// A stale `harness` on PATH from before Phase 6 #6 would resolve as a
-// binary but reject the codex-* subcommands at runtime. The
-// version-gate catches that.
-const MIN_VERSION_WITH_CODEX_SUBCOMMANDS = "0.7.0";
-function defaultVersionProbe(binary) {
-    try {
-        const result = spawnSync(binary, ["--version"], {
-            encoding: "utf8",
-            timeout: 5_000,
-        });
-        if (result.status !== 0 || result.error)
-            return null;
-        return (result.stdout ?? "").trim();
-    }
-    catch {
-        return null;
-    }
-}
-function compareSemver(a, b) {
-    const aa = a.split(".").map((n) => Number.parseInt(n, 10));
-    const bb = b.split(".").map((n) => Number.parseInt(n, 10));
-    const len = Math.max(aa.length, bb.length);
-    for (let i = 0; i < len; i++) {
-        const ai = aa[i] ?? 0;
-        const bi = bb[i] ?? 0;
-        if (Number.isNaN(ai) || Number.isNaN(bi))
-            return 0;
-        if (ai > bi)
-            return 1;
-        if (ai < bi)
-            return -1;
-    }
-    return 0;
-}
-function checkSubcommandsAvailable(harnessBinaryPath, versionProbe) {
-    // When the binary is missing the operator already gets a clear error
-    // from `checkHarnessBinary`; emitting a second cascade-error here
-    // would double-count in `errorCount` for one root cause. Skip
-    // entirely.
-    if (!harnessBinaryPath) {
-        return null;
-    }
-    const stdout = versionProbe(harnessBinaryPath);
-    if (stdout === null) {
-        return {
-            name: "codex-* subcommands",
-            status: "warn",
-            message: `\`${harnessBinaryPath} --version\` did not respond cleanly; cannot confirm the codex-* subcommands are wired (need >= ${MIN_VERSION_WITH_CODEX_SUBCOMMANDS})`,
-        };
-    }
-    const m = stdout.match(/(\d+(?:\.\d+){0,3})/);
-    if (!m || !m[1]) {
-        return {
-            name: "codex-* subcommands",
-            status: "warn",
-            message: `could not parse a version from "${stdout}"; cannot confirm the codex-* subcommands are wired`,
-        };
-    }
-    const actual = m[1];
-    if (compareSemver(actual, MIN_VERSION_WITH_CODEX_SUBCOMMANDS) < 0) {
-        return {
-            name: "codex-* subcommands",
-            status: "error",
-            message: `harness on PATH is v${actual}; codex-* subcommands require >= ${MIN_VERSION_WITH_CODEX_SUBCOMMANDS}. Update the harness install.`,
-        };
-    }
-    // Sanity-check against the version this module is shipped from: if
-    // the harness on PATH is markedly newer or older than the in-process
-    // version, the operator probably has more than one harness install.
-    // Not an error; just informative.
-    const note = actual !== HARNESS_VERSION
-        ? ` (in-process v${HARNESS_VERSION}; mismatch is harmless if intentional)`
-        : "";
-    return {
-        name: "codex-* subcommands",
-        status: "ok",
-        message: `harness on PATH v${actual} >= ${MIN_VERSION_WITH_CODEX_SUBCOMMANDS}${note}`,
-    };
-}
 function checkConfigToml(manifestDir) {
     const target = path.join(manifestDir, CODEX_CONFIG_RELPATH);
     if (!fs.existsSync(target)) {
@@ -217,15 +135,14 @@ function checkConfigToml(manifestDir) {
         message: `present: ${target}`,
     };
 }
-function codexHooksFromManifest(manifest) {
-    const expansion = expandPolicyPacks(manifest, "codex");
-    // The manifest's own hooks[] AND the codex-pack expansion both ship
-    // into the generated TOML, so we check both.
-    const all = [...manifest.hooks, ...expansion.hooks];
-    return all;
-}
-function checkHookCommands(manifest, pathEnv, isExecutable) {
-    const hooks = codexHooksFromManifest(manifest);
+/**
+ * `expansionHooks` are the hooks the codex pack expansion contributes; they
+ * default to the real expansion and are a parameter so a test can feed one
+ * that calls a removed verb.
+ */
+export function checkHookCommands(manifest, pathEnv, isExecutable, expansionHooks = expandPolicyPacks(manifest, "codex").hooks) {
+    const manifestHooks = new Set(manifest.hooks);
+    const hooks = [...manifest.hooks, ...expansionHooks];
     if (hooks.length === 0) {
         return [
             {
@@ -246,14 +163,29 @@ function checkHookCommands(manifest, pathEnv, isExecutable) {
             });
             continue;
         }
+        // A hook that calls a removed verb fails at runtime with "unknown
+        // command", so it must not pass as a healthy harness subcommand below.
+        const removed = invokesRemovedCommand(h.command);
+        if (removed !== undefined) {
+            // A manifest hook is already a manifest warning (hooks[].command), and
+            // doctor counts each site once: this line stays non-ok but is not
+            // tallied again. A pack-expansion hook has no manifest site, so its
+            // warning is the only one and is counted.
+            const fromManifest = manifestHooks.has(h);
+            out.push({
+                name: `hook ${h.name}`,
+                status: "warn",
+                message: removedCommandMessage(removed, `delete hook "${h.name}" from the manifest (and every policy that names it), then re-run \`harness apply --runtime codex\``) + (fromManifest ? " (counted once, in the manifest warnings)" : ""),
+                ...(fromManifest ? { countedElsewhere: true } : {}),
+            });
+            continue;
+        }
         // Bare `harness` subcommands resolve as long as the harness binary
         // does (already checked above); skip the per-hook PATH lookup for
         // them so the error tally doesn't double-count a missing harness.
         // Bare `harness <subcommand>` form: any operator-authored hook that
         // calls into the harness binary lands here, not just pack-contributed
-        // ones. The harness-binary check above is the upstream gate; the
-        // version-gate (`checkSubcommandsAvailable`) catches stale installs
-        // that would reject the subcommand at runtime.
+        // ones. The harness-binary check above is the upstream gate.
         if (h.command.startsWith(HARNESS_COMMAND_PREFIX)) {
             out.push({
                 name: `hook ${h.name}`,
@@ -278,62 +210,17 @@ function checkHookCommands(manifest, pathEnv, isExecutable) {
     }
     return out;
 }
-function checkReportsDir(manifestDir) {
-    // Use the same resolver the rest of the stack uses so the doctor's
-    // reported path agrees with what the Stop hook, PreToolUse blocker
-    // and `harness approve understanding` will actually touch:
-    //   1. UNDERSTANDING_GATE_REPORT_DIR if set,
-    //   2. manifest-anchored fallback otherwise.
-    const dir = defaultReportsDir(manifestDir);
-    // We do NOT require the directory to exist (a fresh project has no
-    // reports yet). What we do require is that we can either create it
-    // or write into it. Best-effort probe: if the parent is writable,
-    // we are fine.
-    const parent = path.dirname(dir);
-    let target;
-    if (fs.existsSync(dir)) {
-        target = dir;
-    }
-    else if (fs.existsSync(parent)) {
-        target = parent;
-    }
-    else {
-        target = manifestDir;
-    }
-    try {
-        fs.accessSync(target, fs.constants.W_OK);
-        return {
-            name: "persisted-report directory",
-            status: "ok",
-            message: fs.existsSync(dir)
-                ? `${dir} writable`
-                : `${dir} not present; ${target} is writable (the directory is created on first report)`,
-        };
-    }
-    catch {
-        return {
-            name: "persisted-report directory",
-            status: "warn",
-            message: `cannot write to ${target}; the Stop-equivalent (when shipped) will fail to capture reports`,
-        };
-    }
-}
 export function runCodexTargetChecks(manifest, opts) {
     const pathEnv = opts.pathEnv ?? process.env["PATH"] ?? "";
     const isExecutable = opts.isExecutable ?? defaultIsExecutable;
-    const versionProbe = opts.versionProbe ?? defaultVersionProbe;
     const checks = [];
     const harnessResult = resolveHarnessBinary({ pathEnv, isExecutable }, opts.harnessBinary);
     checks.push(harnessResult.entry);
-    const subcmdEntry = checkSubcommandsAvailable(harnessResult.resolved, versionProbe);
-    if (subcmdEntry !== null)
-        checks.push(subcmdEntry);
     checks.push(checkConfigToml(opts.manifestDir));
     checks.push(...checkHookCommands(manifest, pathEnv, isExecutable));
-    checks.push(checkReportsDir(opts.manifestDir));
     return { target: "codex", checks };
 }
 export function countCodexDiagnostics(report) {
-    return countStatusDiagnostics(report.checks);
+    return countStatusDiagnostics(report.checks.filter((c) => c.countedElsewhere !== true));
 }
 //# sourceMappingURL=codex.js.map

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@@ -1 +1 @@
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