@rotifer/playground 0.8.0 → 0.8.5

package/dist/utils/binding.js

@@ -4,16 +4,17 @@ exports.tryLoadBinding = tryLoadBinding;
 exports.isNativeAvailable = isNativeAvailable;
 const node_path_1 = require("node:path");
 const node_fs_1 = require("node:fs");
+const private_fs_js_1 = require("./private-fs.js");
 let _binding = null;
-let _loadAttempted = false;
+let _hasLoadAttempted = false;
 /**
  * Try to load the napi native addon.
  * Returns null if the addon is not available (fallback to pure-TS path).
  */
 function tryLoadBinding() {
-    if (_loadAttempted)
+    if (_hasLoadAttempted)
         return _binding;
-    _loadAttempted = true;
+    _hasLoadAttempted = true;
     const candidates = [
         (0, node_path_1.join)(__dirname, "..", "..", "index.darwin-arm64.node"),
         (0, node_path_1.join)(__dirname, "..", "..", "index.darwin-x64.node"),
@@ -27,7 +28,7 @@ function tryLoadBinding() {
                 const mod = require(candidate);
                 if (mod.PlaygroundBinding) {
                     const tmpDir = (0, node_path_1.join)(process.env.HOME || process.env.USERPROFILE || "/tmp", ".rotifer", "napi-binding");
-                    require("node:fs").mkdirSync(tmpDir, { recursive: true });
+                    (0, private_fs_js_1.ensurePrivateDir)(tmpDir);
                     const instance = new mod.PlaygroundBinding(tmpDir);
                     _binding = instance;
                     return _binding;

package/dist/utils/binding.js.map

@@ -1 +1 @@
-{"version":3,"file":"binding.js","sourceRoot":"","sources":["../../src/utils/binding.ts"],"names":[],"mappings":";;AAuEA,wCAkCC;AAED,8CAEC;AA7GD,yCAAiC;AACjC,qCAAqC;AA+DrC,IAAI,QAAQ,GAAyB,IAAI,CAAC;AAC1C,IAAI,cAAc,GAAG,KAAK,CAAC;AAE3B;;;GAGG;AACH,SAAgB,cAAc;IAC5B,IAAI,cAAc;QAAE,OAAO,QAAQ,CAAC;IACpC,cAAc,GAAG,IAAI,CAAC;IAEtB,MAAM,UAAU,GAAG;QACjB,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,yBAAyB,CAAC;QACtD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,uBAAuB,CAAC;QACpD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,0BAA0B,CAAC;QACvD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,2BAA2B,CAAC;QACxD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,gBAAgB,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,IAAI,OAAO,CAAC;KACrF,CAAC;IAEF,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,IAAI,IAAA,oBAAU,EAAC,SAAS,CAAC,EAAE,CAAC;YAC1B,IAAI,CAAC;gBACH,MAAM,GAAG,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC;gBAC/B,IAAI,GAAG,CAAC,iBAAiB,EAAE,CAAC;oBAC1B,MAAM,MAAM,GAAG,IAAA,gBAAI,EACjB,OAAO,CAAC,GAAG,CAAC,IAAI,IAAI,OAAO,CAAC,GAAG,CAAC,WAAW,IAAI,MAAM,EACrD,UAAU,EACV,cAAc,CACf,CAAC;oBACF,OAAO,CAAC,SAAS,CAAC,CAAC,SAAS,CAAC,MAAM,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;oBAC1D,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAC;oBACnD,QAAQ,GAAG,QAAyB,CAAC;oBACrC,OAAO,QAAQ,CAAC;gBAClB,CAAC;YACH,CAAC;YAAC,MAAM,CAAC;gBACP,6CAA6C;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAgB,iBAAiB;IAC/B,OAAO,cAAc,EAAE,KAAK,IAAI,CAAC;AACnC,CAAC"}
+{"version":3,"file":"binding.js","sourceRoot":"","sources":["../../src/utils/binding.ts"],"names":[],"mappings":";;AAwEA,wCAkCC;AAED,8CAEC;AA9GD,yCAAiC;AACjC,qCAAqC;AACrC,mDAAmD;AA+DnD,IAAI,QAAQ,GAAyB,IAAI,CAAC;AAC1C,IAAI,iBAAiB,GAAG,KAAK,CAAC;AAE9B;;;GAGG;AACH,SAAgB,cAAc;IAC5B,IAAI,iBAAiB;QAAE,OAAO,QAAQ,CAAC;IACvC,iBAAiB,GAAG,IAAI,CAAC;IAEzB,MAAM,UAAU,GAAG;QACjB,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,yBAAyB,CAAC;QACtD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,uBAAuB,CAAC;QACpD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,0BAA0B,CAAC;QACvD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,2BAA2B,CAAC;QACxD,IAAA,gBAAI,EAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,gBAAgB,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,IAAI,OAAO,CAAC;KACrF,CAAC;IAEF,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,IAAI,IAAA,oBAAU,EAAC,SAAS,CAAC,EAAE,CAAC;YAC1B,IAAI,CAAC;gBACH,MAAM,GAAG,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC;gBAC/B,IAAI,GAAG,CAAC,iBAAiB,EAAE,CAAC;oBAC1B,MAAM,MAAM,GAAG,IAAA,gBAAI,EACjB,OAAO,CAAC,GAAG,CAAC,IAAI,IAAI,OAAO,CAAC,GAAG,CAAC,WAAW,IAAI,MAAM,EACrD,UAAU,EACV,cAAc,CACf,CAAC;oBACF,IAAA,gCAAgB,EAAC,MAAM,CAAC,CAAC;oBACzB,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAC;oBACnD,QAAQ,GAAG,QAAyB,CAAC;oBACrC,OAAO,QAAQ,CAAC;gBAClB,CAAC;YACH,CAAC;YAAC,MAAM,CAAC;gBACP,6CAA6C;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAgB,iBAAiB;IAC/B,OAAO,cAAc,EAAE,KAAK,IAAI,CAAC;AACnC,CAAC"}

package/dist/utils/content-hash.d.ts

@@ -0,0 +1,3 @@
+export declare function canonicalSerialize(phenotype: Record<string, unknown>): string;
+export declare function contentHash(phenotype: Record<string, unknown>): string;
+//# sourceMappingURL=content-hash.d.ts.map

package/dist/utils/content-hash.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"content-hash.d.ts","sourceRoot":"","sources":["../../src/utils/content-hash.ts"],"names":[],"mappings":"AAYA,wBAAgB,kBAAkB,CAChC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACjC,MAAM,CAER;AAED,wBAAgB,WAAW,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAItE"}

package/dist/utils/content-hash.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.canonicalSerialize = canonicalSerialize;
+exports.contentHash = contentHash;
+const node_crypto_1 = require("node:crypto");
+function sortKeysDeep(obj) {
+    if (obj === null || typeof obj !== "object")
+        return obj;
+    if (Array.isArray(obj))
+        return obj.map(sortKeysDeep);
+    const sorted = {};
+    for (const key of Object.keys(obj).sort()) {
+        sorted[key] = sortKeysDeep(obj[key]);
+    }
+    return sorted;
+}
+function canonicalSerialize(phenotype) {
+    return JSON.stringify(sortKeysDeep(phenotype));
+}
+function contentHash(phenotype) {
+    return (0, node_crypto_1.createHash)("sha256")
+        .update(canonicalSerialize(phenotype))
+        .digest("hex");
+}
+//# sourceMappingURL=content-hash.js.map

package/dist/utils/content-hash.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"content-hash.js","sourceRoot":"","sources":["../../src/utils/content-hash.ts"],"names":[],"mappings":";;AAYA,gDAIC;AAED,kCAIC;AAtBD,6CAAyC;AAEzC,SAAS,YAAY,CAAC,GAAY;IAChC,IAAI,GAAG,KAAK,IAAI,IAAI,OAAO,GAAG,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC;IACxD,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;IACrD,MAAM,MAAM,GAA4B,EAAE,CAAC;IAC3C,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,GAA8B,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC;QACrE,MAAM,CAAC,GAAG,CAAC,GAAG,YAAY,CAAE,GAA+B,CAAC,GAAG,CAAC,CAAC,CAAC;IACpE,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAgB,kBAAkB,CAChC,SAAkC;IAElC,OAAO,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC;AACjD,CAAC;AAED,SAAgB,WAAW,CAAC,SAAkC;IAC5D,OAAO,IAAA,wBAAU,EAAC,QAAQ,CAAC;SACxB,MAAM,CAAC,kBAAkB,CAAC,SAAS,CAAC,CAAC;SACrC,MAAM,CAAC,KAAK,CAAC,CAAC;AACnB,CAAC"}

package/dist/utils/display.d.ts

@@ -1,9 +1,18 @@
+import type { Command, Help } from "commander";
+export type OutputMode = "human" | "json" | "plain";
+export declare function setOutputMode(mode: OutputMode): void;
+export declare function getOutputMode(): OutputMode;
+export declare function isJsonMode(): boolean;
 export declare function success(message: string): void;
 export declare function error(message: string, detail?: string): void;
 export declare function info(message: string): void;
 export declare function warn(message: string): void;
-export declare function header(title: string): void;
+export declare function hint(message: string): void;
+export declare function header(title: string, opts?: {
+    separator?: boolean;
+}): void;
 export declare function keyValue(key: string, value: string): void;
+export declare const kv: typeof keyValue;
 export declare function geneId(id: string): string;
 export declare function rustStyleError(opts: {
     code: string;
@@ -13,4 +22,38 @@ export declare function rustStyleError(opts: {
     suggestion?: string;
     docsUrl?: string;
 }): void;
+export declare function link(text: string, url: string): string;
+export interface Spinner {
+    stop(successMessage?: string): void;
+    update(message: string): void;
+}
+export declare function spinner(message: string): Spinner;
+export declare function banner(version: string): string;
+export declare function formatGroupedHelp(cmd: Command, helper: Help): string;
+export declare function formatSubcommandHelp(cmd: Command, helper: Help): string;
+export declare function welcomeBanner(opts: {
+    version: string;
+    message?: string;
+    hints?: Array<[string, string]>;
+    docsUrl?: string;
+}): void;
+export declare function box(lines: string[], opts?: {
+    title?: string;
+}): void;
+export interface TableColumn<T = Record<string, unknown>> {
+    key: string;
+    label: string;
+    width?: number;
+    align?: "left" | "right";
+    format?: (value: unknown, row: T) => string;
+}
+export declare function table<T extends Record<string, unknown>>(data: T[], columns: TableColumn<T>[]): void;
+export declare function barChart(items: {
+    label: string;
+    value: number;
+}[], opts?: {
+    barWidth?: number;
+}): void;
+export declare function renderResult<T>(data: T, humanRenderer: (data: T) => void): void;
+export declare function stripAnsi(str: string): string;
 //# sourceMappingURL=display.d.ts.map

package/dist/utils/display.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"display.d.ts","sourceRoot":"","sources":["../../src/utils/display.ts"],"names":[],"mappings":"AAEA,wBAAgB,OAAO,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE7C;AAED,wBAAgB,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAK5D;AAED,wBAAgB,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE1C;AAED,wBAAgB,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE1C;AAED,wBAAgB,MAAM,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAI1C;AAED,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,IAAI,CAEzD;AAED,wBAAgB,MAAM,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAEzC;AAED,wBAAgB,cAAc,CAAC,IAAI,EAAE;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,GAAG,IAAI,CAoBP"}
+{"version":3,"file":"display.d.ts","sourceRoot":"","sources":["../../src/utils/display.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAK/C,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,MAAM,GAAG,OAAO,CAAC;AAIpD,wBAAgB,aAAa,CAAC,IAAI,EAAE,UAAU,GAAG,IAAI,CAKpD;AAED,wBAAgB,aAAa,IAAI,UAAU,CAE1C;AAED,wBAAgB,UAAU,IAAI,OAAO,CAEpC;AAID,wBAAgB,OAAO,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE7C;AAED,wBAAgB,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAK5D;AAED,wBAAgB,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE1C;AAED,wBAAgB,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE1C;AAED,wBAAgB,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAE1C;AAID,wBAAgB,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE;IAAE,SAAS,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,IAAI,CAM1E;AAID,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,IAAI,CAEzD;AAED,eAAO,MAAM,EAAE,iBAAW,CAAC;AAI3B,wBAAgB,MAAM,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAGzC;AAID,wBAAgB,cAAc,CAAC,IAAI,EAAE;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,GAAG,IAAI,CAkBP;AAID,wBAAgB,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,CAItD;AAID,MAAM,WAAW,OAAO;IACtB,IAAI,CAAC,cAAc,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC,MAAM,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED,wBAAgB,OAAO,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAiChD;AAID,wBAAgB,MAAM,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAiB9C;AA2BD,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,GAAG,MAAM,CAmEpE;AAID,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,GAAG,MAAM,CAiDvE;AAYD,wBAAgB,aAAa,CAAC,IAAI,EAAE;IAClC,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC;IAChC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,GAAG,IAAI,CAsCP;AAID,wBAAgB,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,IAAI,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAkBpE;AAID,MAAM,WAAW,WAAW,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC;IACtD,GAAG,EAAE,MAAM,CAAC;IACZ,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IACzB,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,MAAM,CAAC;CAC7C;AAED,wBAAgB,KAAK,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrD,IAAI,EAAE,CAAC,EAAE,EACT,OAAO,EAAE,WAAW,CAAC,CAAC,CAAC,EAAE,GACxB,IAAI,CAqEN;AAID,wBAAgB,QAAQ,CACtB,KAAK,EAAE;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,EAAE,EACzC,IAAI,GAAE;IAAE,QAAQ,CAAC,EAAE,MAAM,CAAA;CAAO,GAC/B,IAAI,CAYN;AAID,wBAAgB,YAAY,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,IAAI,GAAG,IAAI,CAM/E;AAuDD,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAE7C"}

package/dist/utils/display.js

@@ -3,54 +3,483 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.kv = void 0;
+exports.setOutputMode = setOutputMode;
+exports.getOutputMode = getOutputMode;
+exports.isJsonMode = isJsonMode;
 exports.success = success;
 exports.error = error;
 exports.info = info;
 exports.warn = warn;
+exports.hint = hint;
 exports.header = header;
 exports.keyValue = keyValue;
 exports.geneId = geneId;
 exports.rustStyleError = rustStyleError;
+exports.link = link;
+exports.spinner = spinner;
+exports.banner = banner;
+exports.formatGroupedHelp = formatGroupedHelp;
+exports.formatSubcommandHelp = formatSubcommandHelp;
+exports.welcomeBanner = welcomeBanner;
+exports.box = box;
+exports.table = table;
+exports.barChart = barChart;
+exports.renderResult = renderResult;
+exports.stripAnsi = stripAnsi;
 const chalk_1 = __importDefault(require("chalk"));
+const palette_js_1 = require("./palette.js");
+let _mode = "human";
+function setOutputMode(mode) {
+    _mode = mode;
+    if (mode === "plain" || mode === "json") {
+        chalk_1.default.level = 0;
+    }
+}
+function getOutputMode() {
+    return _mode;
+}
+function isJsonMode() {
+    return _mode === "json";
+}
+// ── Semantic messages ────────────────────────────────────────
 function success(message) {
-    console.log(chalk_1.default.green("✓") + " " + message);
+    console.log(palette_js_1.c.success(palette_js_1.icon.success) + " " + message);
 }
 function error(message, detail) {
-    console.error(chalk_1.default.red("✗") + " " + chalk_1.default.red(message));
+    console.error(palette_js_1.c.error(palette_js_1.icon.error) + " " + palette_js_1.c.error(message));
     if (detail) {
-        console.error(chalk_1.default.dim("  → " + detail));
+        console.error(palette_js_1.c.muted("  " + palette_js_1.icon.arrow + " " + detail));
     }
 }
 function info(message) {
-    console.log(chalk_1.default.blue("ℹ") + " " + message);
+    console.log(palette_js_1.c.info(palette_js_1.icon.info) + " " + message);
 }
 function warn(message) {
-    console.log(chalk_1.default.yellow("⚠") + " " + message);
+    console.log(palette_js_1.c.warn(palette_js_1.icon.warn) + " " + message);
+}
+function hint(message) {
+    console.log(palette_js_1.c.muted(palette_js_1.icon.info) + " " + palette_js_1.c.muted(message));
 }
-function header(title) {
+// ── Header ───────────────────────────────────────────────────
+function header(title, opts) {
     console.log();
-    console.log(chalk_1.default.bold.cyan(`  ${title}`));
-    console.log(chalk_1.default.dim("  " + "─".repeat(title.length + 2)));
+    console.log(palette_js_1.c.accent.bold(`  ${title}`));
+    if (opts?.separator !== false) {
+        console.log(palette_js_1.c.muted("  " + palette_js_1.icon.dash.repeat(title.length + 2)));
+    }
 }
+// ── Key-Value ────────────────────────────────────────────────
 function keyValue(key, value) {
-    console.log(`  ${chalk_1.default.dim(key + ":")} ${value}`);
+    console.log(`  ${palette_js_1.c.accent(key + ":")} ${value}`);
 }
+exports.kv = keyValue;
+// ── Gene ID formatter ────────────────────────────────────────
 function geneId(id) {
-    return chalk_1.default.yellow(id.slice(0, 12) + "…");
+    if (id.length <= 12)
+        return palette_js_1.c.warn(id);
+    return palette_js_1.c.warn(id.slice(0, 12) + "…");
 }
+// ── Rust-style error ─────────────────────────────────────────
 function rustStyleError(opts) {
     console.error();
-    console.error(chalk_1.default.red.bold(`error[${opts.code}]`) + chalk_1.default.bold(`: ${opts.message}`));
+    console.error(palette_js_1.c.error.bold(`error[${opts.code}]`) + palette_js_1.c.bold(`: ${opts.message}`));
     if (opts.file) {
-        console.error(chalk_1.default.blue(" --> ") + opts.file + (opts.line ? `:${opts.line}` : ""));
+        console.error(palette_js_1.c.info(" --> ") + opts.file + (opts.line ? `:${opts.line}` : ""));
     }
     if (opts.suggestion) {
         console.error();
-        console.error(chalk_1.default.green("help") + `: ${opts.suggestion}`);
+        console.error(palette_js_1.c.success("help") + `: ${opts.suggestion}`);
     }
     if (opts.docsUrl) {
-        console.error(chalk_1.default.dim("docs") + `: ${opts.docsUrl}`);
+        console.error(palette_js_1.c.muted("docs") + `: ${link(opts.docsUrl, opts.docsUrl)}`);
     }
     console.error();
 }
+// ── OSC-8 Hyperlink ──────────────────────────────────────────
+function link(text, url) {
+    if (!process.stderr.isTTY && !process.stdout.isTTY)
+        return `${text} (${url})`;
+    if (chalk_1.default.level === 0)
+        return `${text} (${url})`;
+    return `\x1b]8;;${url}\x07${text}\x1b]8;;\x07`;
+}
+function spinner(message) {
+    if (!process.stderr.isTTY || _mode !== "human") {
+        process.stderr.write(message + "\n");
+        return {
+            update() { },
+            stop(finalMessage) {
+                if (finalMessage)
+                    console.log(finalMessage);
+            },
+        };
+    }
+    const frames = ["◒", "◐", "◓", "◑"];
+    let frame = 0;
+    let msg = message;
+    const write = (text) => process.stderr.write(text);
+    write(`  ${palette_js_1.c.accent(frames[0])} ${msg}`);
+    const interval = setInterval(() => {
+        frame = (frame + 1) % frames.length;
+        write(`\x1b[2K\r  ${palette_js_1.c.accent(frames[frame])} ${msg}`);
+    }, 80);
+    return {
+        update(newMessage) {
+            msg = newMessage;
+        },
+        stop(finalMessage) {
+            clearInterval(interval);
+            write("\x1b[2K\r");
+            if (finalMessage)
+                console.log(finalMessage);
+        },
+    };
+}
+// ── Brand Banner ─────────────────────────────────────────────
+function banner(version) {
+    const argv = process.argv;
+    if (_mode !== "human" || argv.includes("--plain") || argv.includes("--json")) {
+        return "";
+    }
+    const v = palette_js_1.c.muted(`v${version}`);
+    const tagline = palette_js_1.c.muted("Code as Gene");
+    const sep = palette_js_1.c.accentDim("─".repeat(32));
+    return [
+        "",
+        `  ${palette_js_1.c.accent.bold("◎")} ${palette_js_1.c.accent.bold("Rotifer Protocol")}  ${v}`,
+        `  ${sep}`,
+        `  ${tagline}`,
+        "",
+    ].join("\n");
+}
+// ── Grouped Help Formatter (A/C/D) ──────────────────────────
+const COMMAND_GROUPS = [
+    {
+        label: "Development",
+        names: ["init", "scan", "wrap", "test", "compile", "run", "list"],
+    },
+    {
+        label: "Cloud",
+        names: ["login", "logout", "publish", "search", "install"],
+    },
+    {
+        label: "Discovery",
+        names: ["info", "stats", "compare", "reputation", "versions"],
+    },
+    {
+        label: "Arena & Agents",
+        names: ["arena", "agent"],
+    },
+    {
+        label: "Tools",
+        names: ["vg", "network", "self-update", "config", "whoami"],
+    },
+];
+function formatGroupedHelp(cmd, helper) {
+    const isPlain = _mode === "plain" || process.argv.includes("--plain");
+    const lines = [];
+    lines.push(`Usage: ${helper.commandUsage(cmd)}`);
+    lines.push("");
+    const desc = helper.commandDescription(cmd);
+    if (desc) {
+        lines.push(desc);
+        lines.push("");
+    }
+    const opts = helper.visibleOptions(cmd);
+    if (opts.length > 0) {
+        lines.push(isPlain ? "Options:" : palette_js_1.c.accent.bold("Options:"));
+        const optWidth = helper.padWidth(cmd, helper);
+        for (const opt of opts) {
+            const term = helper.optionTerm(opt).padEnd(optWidth + 2);
+            const desc_ = helper.optionDescription(opt);
+            lines.push(isPlain ? `  ${term} ${desc_}` : `  ${term} ${palette_js_1.c.muted(desc_)}`);
+        }
+        lines.push("");
+    }
+    const allCmds = helper.visibleCommands(cmd);
+    const cmdMap = new Map();
+    for (const sub of allCmds)
+        cmdMap.set(sub.name(), sub);
+    const placed = new Set();
+    for (const group of COMMAND_GROUPS) {
+        const members = group.names.filter((n) => cmdMap.has(n));
+        if (members.length === 0)
+            continue;
+        lines.push(isPlain ? `${group.label}:` : palette_js_1.c.accent.bold(`${group.label}:`));
+        for (const name of members) {
+            const sub = cmdMap.get(name);
+            const usage = helper.subcommandTerm(sub);
+            const desc_ = helper.subcommandDescription(sub);
+            const padded = usage.padEnd(34);
+            lines.push(isPlain ? `  ${padded} ${desc_}` : `  ${padded} ${palette_js_1.c.muted(desc_)}`);
+            placed.add(name);
+        }
+        lines.push("");
+    }
+    const ungrouped = allCmds.filter((sub) => !placed.has(sub.name()));
+    if (ungrouped.length > 0) {
+        lines.push(isPlain ? "Other:" : palette_js_1.c.accent.bold("Other:"));
+        for (const sub of ungrouped) {
+            const usage = helper.subcommandTerm(sub);
+            const desc_ = helper.subcommandDescription(sub);
+            lines.push(`  ${usage.padEnd(34)} ${palette_js_1.c.muted(desc_)}`);
+        }
+        lines.push("");
+    }
+    if (isPlain) {
+        lines.push("Run rotifer <command> --help for detailed usage.");
+    }
+    else {
+        lines.push(palette_js_1.c.muted("Run ") + palette_js_1.c.accent("rotifer <command> --help") + palette_js_1.c.muted(" for detailed usage."));
+    }
+    lines.push("");
+    return lines.join("\n");
+}
+// ── Subcommand Help Formatter ─────────────────────────────────
+function formatSubcommandHelp(cmd, helper) {
+    const isPlain = _mode === "plain" || process.argv.includes("--plain");
+    const lines = [];
+    lines.push(`Usage: ${helper.commandUsage(cmd)}`);
+    lines.push("");
+    const desc = helper.commandDescription(cmd);
+    if (desc) {
+        lines.push(desc);
+        lines.push("");
+    }
+    const args = cmd.registeredArguments;
+    if (args.length > 0) {
+        lines.push(isPlain ? "Arguments:" : palette_js_1.c.accent.bold("Arguments:"));
+        const argWidth = Math.max(...args.map((a) => a.name().length)) + 4;
+        for (const arg of args) {
+            const term = arg.name().padEnd(argWidth);
+            const argDesc = arg.description || "";
+            lines.push(isPlain ? `  ${term} ${argDesc}` : `  ${term} ${palette_js_1.c.muted(argDesc)}`);
+        }
+        lines.push("");
+    }
+    const opts = helper.visibleOptions(cmd);
+    if (opts.length > 0) {
+        lines.push(isPlain ? "Options:" : palette_js_1.c.accent.bold("Options:"));
+        const optWidth = helper.padWidth(cmd, helper);
+        for (const opt of opts) {
+            const term = helper.optionTerm(opt).padEnd(optWidth + 2);
+            const optDesc = helper.optionDescription(opt);
+            lines.push(isPlain ? `  ${term} ${optDesc}` : `  ${term} ${palette_js_1.c.muted(optDesc)}`);
+        }
+        lines.push("");
+    }
+    const subCmds = helper.visibleCommands(cmd);
+    if (subCmds.length > 0) {
+        lines.push(isPlain ? "Commands:" : palette_js_1.c.accent.bold("Commands:"));
+        for (const sub of subCmds) {
+            const usage = helper.subcommandTerm(sub);
+            const subDesc = helper.subcommandDescription(sub);
+            lines.push(isPlain ? `  ${usage.padEnd(30)} ${subDesc}` : `  ${usage.padEnd(30)} ${palette_js_1.c.muted(subDesc)}`);
+        }
+        lines.push("");
+    }
+    return lines.join("\n");
+}
+// ── Welcome Banner (ASCII Art) ───────────────────────────────
+const ASCII_LOGO_LINES = [
+    "   ____       _   _  __",
+    "  |  _ \\ ___ | |_(_)/ _| ___ _ __",
+    "  | |_) / _ \\| __| | |_ / _ \\ '__|",
+    "  |  _ < (_) | |_| |  _|  __/ |",
+    "  |_| \\_\\___/ \\__|_|_|  \\___|_|",
+];
+function welcomeBanner(opts) {
+    if (_mode === "json" || process.argv.includes("--json"))
+        return;
+    if (process.env.CI)
+        return;
+    const isPlain = _mode === "plain" || process.argv.includes("--plain");
+    const last = ASCII_LOGO_LINES.length - 1;
+    console.log();
+    for (let i = 0; i < ASCII_LOGO_LINES.length; i++) {
+        const suffix = i === last ? `   v${opts.version}` : "";
+        const line = ASCII_LOGO_LINES[i] + suffix;
+        console.log(isPlain ? `  ${line}` : `  ${palette_js_1.c.accent(line)}`);
+    }
+    console.log();
+    if (opts.message) {
+        console.log(isPlain ? `  ${opts.message}` : `  ${palette_js_1.c.bold(opts.message)}`);
+        console.log();
+    }
+    if (opts.hints && opts.hints.length > 0) {
+        for (const [cmd, desc] of opts.hints) {
+            const padded = cmd.padEnd(28);
+            console.log(isPlain ? `    ${padded} ${desc}` : `    ${palette_js_1.c.accent(padded)} ${palette_js_1.c.muted(desc)}`);
+        }
+        console.log();
+    }
+    if (opts.docsUrl) {
+        console.log(isPlain
+            ? `  Docs: ${opts.docsUrl}`
+            : `  ${palette_js_1.c.muted("Docs:")} ${link("rotifer.dev/docs", opts.docsUrl)}`);
+        console.log();
+    }
+}
+// ── Box ──────────────────────────────────────────────────────
+function box(lines, opts) {
+    const allLines = opts?.title ? [palette_js_1.c.bold(opts.title), "", ...lines] : lines;
+    const maxLen = Math.max(...allLines.map((l) => stripAnsi(l).length), 20);
+    const innerW = maxLen + 2;
+    const top = palette_js_1.c.muted(`  ┌${"─".repeat(innerW)}┐`);
+    const bot = palette_js_1.c.muted(`  └${"─".repeat(innerW)}┘`);
+    const empty = palette_js_1.c.muted("  │") + " ".repeat(innerW) + palette_js_1.c.muted("│");
+    console.log(top);
+    console.log(empty);
+    for (const line of allLines) {
+        const vis = stripAnsi(line).length;
+        const right = innerW - vis - 1;
+        console.log(palette_js_1.c.muted("  │") + " " + line + " ".repeat(Math.max(right, 0)) + palette_js_1.c.muted("│"));
+    }
+    console.log(empty);
+    console.log(bot);
+}
+function table(data, columns) {
+    if (data.length === 0)
+        return;
+    const termWidth = process.stdout.columns || 120;
+    const indent = 2;
+    const widths = columns.map((col) => {
+        const headerLen = col.label.length;
+        const maxDataLen = data.reduce((max, row) => {
+            const raw = col.format
+                ? stripAnsi(col.format(row[col.key], row))
+                : String(row[col.key] ?? "");
+            return Math.max(max, raw.length);
+        }, 0);
+        const autoWidth = Math.max(headerLen, maxDataLen) + 2;
+        return col.width ? Math.max(col.width, autoWidth) : autoWidth;
+    });
+    const totalWidth = widths.reduce((a, b) => a + b, 0) + indent;
+    if (totalWidth > termWidth) {
+        const overflow = totalWidth - termWidth;
+        let remaining = overflow;
+        const sorted = widths
+            .map((w, i) => ({ w, i }))
+            .sort((a, b) => b.w - a.w);
+        for (const entry of sorted) {
+            if (remaining <= 0)
+                break;
+            const minW = Math.max(stripAnsi(columns[entry.i].label).length + 2, 6);
+            const canShrink = entry.w - minW;
+            if (canShrink <= 0)
+                continue;
+            const shrink = Math.min(canShrink, remaining);
+            widths[entry.i] -= shrink;
+            remaining -= shrink;
+        }
+        if (remaining > 0) {
+            const fallbackOrder = widths
+                .map((w, i) => ({ w, i }))
+                .sort((a, b) => b.w - a.w);
+            while (remaining > 0) {
+                let didShrink = false;
+                for (const entry of fallbackOrder) {
+                    if (widths[entry.i] <= 1)
+                        continue;
+                    widths[entry.i] -= 1;
+                    remaining -= 1;
+                    didShrink = true;
+                    if (remaining <= 0)
+                        break;
+                }
+                if (!didShrink)
+                    break;
+            }
+        }
+    }
+    const headerLine = columns
+        .map((col, i) => pad(col.label, widths[i], col.align))
+        .join("");
+    console.log("  " + palette_js_1.c.accent(headerLine));
+    console.log("  " + palette_js_1.c.accentDim(palette_js_1.icon.dash.repeat(widths.reduce((a, b) => a + b, 0))));
+    for (const row of data) {
+        const cells = columns.map((col, i) => {
+            const formatted = col.format
+                ? col.format(row[col.key], row)
+                : String(row[col.key] ?? "");
+            return pad(formatted, widths[i], col.align);
+        });
+        console.log("  " + cells.join(""));
+    }
+}
+// ── Bar chart ────────────────────────────────────────────────
+function barChart(items, opts = {}) {
+    const barWidth = opts.barWidth ?? 30;
+    const max = Math.max(...items.map((i) => i.value), 1);
+    const maxLabelLen = Math.max(...items.map((i) => i.label.length));
+    for (const item of items) {
+        const ratio = item.value / max;
+        const filled = Math.round(ratio * barWidth);
+        const bar = palette_js_1.c.accent("█".repeat(filled)) + palette_js_1.c.muted("░".repeat(barWidth - filled));
+        const label = item.label.padEnd(maxLabelLen);
+        console.log(`  ${label}  ${bar}  ${palette_js_1.c.bold(String(item.value))}`);
+    }
+}
+// ── Data-first rendering ─────────────────────────────────────
+function renderResult(data, humanRenderer) {
+    if (isJsonMode()) {
+        process.stdout.write(JSON.stringify(data, null, 2) + "\n");
+        return;
+    }
+    humanRenderer(data);
+}
+// ── Internal utilities ───────────────────────────────────────
+function truncateAnsi(str, maxVisible) {
+    let visible = 0;
+    let i = 0;
+    let result = "";
+    let hasAnsi = false;
+    const len = str.length;
+    while (i < len && visible < maxVisible) {
+        if (str[i] === "\x1b") {
+            if (str[i + 1] === "[") {
+                const end = str.indexOf("m", i);
+                if (end !== -1) {
+                    result += str.slice(i, end + 1);
+                    i = end + 1;
+                    hasAnsi = true;
+                    continue;
+                }
+            }
+            else if (str[i + 1] === "]") {
+                const end = str.indexOf("\x07", i);
+                if (end !== -1) {
+                    result += str.slice(i, end + 1);
+                    i = end + 1;
+                    hasAnsi = true;
+                    continue;
+                }
+            }
+        }
+        result += str[i];
+        visible++;
+        i++;
+    }
+    return hasAnsi ? result + "\x1b[0m" : result;
+}
+function pad(str, width, align = "left") {
+    const visible = stripAnsi(str).length;
+    if (visible >= width) {
+        if (width <= 2)
+            return stripAnsi(str).slice(0, width);
+        const truncated = truncateAnsi(str, width - 2);
+        const truncVisible = stripAnsi(truncated).length;
+        return truncated + "…" + " ".repeat(Math.max(width - truncVisible - 1, 0));
+    }
+    const diff = width - visible;
+    if (align === "right") {
+        const trailing = Math.min(2, diff);
+        return " ".repeat(diff - trailing) + str + " ".repeat(trailing);
+    }
+    return str + " ".repeat(diff);
+}
+function stripAnsi(str) {
+    return str.replace(/\x1b\[[0-9;]*m|\x1b\]8;;[^\x07]*\x07/g, "");
+}
 //# sourceMappingURL=display.js.map