copilot-hub 0.1.29 → 0.1.30

package/apps/agent-engine/.env.example

@@ -1,8 +1,8 @@
-# Runtime state files
-BOT_DATA_DIR=./data
-BOT_REGISTRY_FILE=./data/bot-registry.json
-SECRET_STORE_FILE=./data/secrets.json
-
+# Runtime state files are managed automatically by copilot-hub.
+# Override only if you intentionally want a custom location.
+# BOT_DATA_DIR=
+# BOT_REGISTRY_FILE=
+# SECRET_STORE_FILE=
 
 # Worker defaults
 # If empty, runtime uses Desktop/copilot_workspaces by default
@@ -27,7 +27,7 @@ SHARED_THREAD_ID=shared-main
 TELEGRAM_ALLOWED_CHAT_IDS=
 
 INSTANCE_LOCK_ENABLED=true
-INSTANCE_LOCK_FILE=./data/runtime.lock
+# INSTANCE_LOCK_FILE=
 
 WEB_HOST=127.0.0.1
 WEB_PORT=8787
@@ -37,5 +37,3 @@ WEB_PORT_SEARCH_MAX=30
 
 # Optional worker token environment variables used in bot-registry.json
 TELEGRAM_TOKEN_AGENT_1=
-
-

package/apps/agent-engine/dist/config.js

@@ -134,6 +134,13 @@ export const config = {
 function loadEnvironment() {
     return loadCopilotHubEnvironment({
         cwd: process.cwd(),
+        preserveExistingKeys: [
+            "BOT_DATA_DIR",
+            "BOT_REGISTRY_FILE",
+            "SECRET_STORE_FILE",
+            "INSTANCE_LOCK_FILE",
+            "COPILOT_HUB_HOME_DIR",
+        ],
     });
 }
 function resolveCodexBin(rawValue) {

package/apps/control-plane/.env.example

@@ -4,7 +4,8 @@ HUB_ID=copilot_hub
 HUB_NAME=Copilot Hub
 # Optional. If empty, defaults to Desktop/copilot_workspaces (Windows/macOS/Linux)
 HUB_WORKSPACE_ROOT=
-HUB_DATA_DIR=./data/copilot_hub
+# Runtime state paths are managed automatically by copilot-hub.
+# HUB_DATA_DIR=
 HUB_THREAD_MODE=per_chat
 HUB_SHARED_THREAD_ID=shared-copilot-hub
 HUB_ALLOWED_CHAT_IDS=

package/apps/control-plane/dist/config.js

@@ -141,6 +141,14 @@ export const config = {
 function loadEnvironment() {
     return loadCopilotHubEnvironment({
         cwd: process.cwd(),
+        preserveExistingKeys: [
+            "BOT_DATA_DIR",
+            "BOT_REGISTRY_FILE",
+            "SECRET_STORE_FILE",
+            "INSTANCE_LOCK_FILE",
+            "HUB_DATA_DIR",
+            "COPILOT_HUB_HOME_DIR",
+        ],
     });
 }
 function resolveCodexBin(rawValue) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "copilot-hub",
-  "version": "0.1.29",
+  "version": "0.1.30",
   "description": "Copilot Hub CLI and runtime bundle",
   "license": "MIT",
   "repository": {
@@ -58,6 +58,7 @@
     "status": "npm run build:scripts --silent && node scripts/dist/cli.mjs status",
     "logs": "npm run build:scripts --silent && node scripts/dist/cli.mjs logs",
     "configure": "npm run build:scripts --silent && node scripts/dist/cli.mjs configure",
+    "reset-config": "npm run build:scripts --silent && node scripts/dist/cli.mjs reset-config",
     "test:scripts": "npm run build:scripts --silent && node --test scripts/test/*.test.mjs",
     "test": "npm run test:scripts && npm run test --workspaces --if-present",
     "lint": "eslint .",

package/packages/core/dist/env-config.d.ts

@@ -4,7 +4,8 @@ export interface LoadedCopilotHubEnvironment {
     fileValues: Record<string, string>;
     overriddenKeys: string[];
 }
-export declare function loadCopilotHubEnvironment({ env, cwd, }?: {
+export declare function loadCopilotHubEnvironment({ env, cwd, preserveExistingKeys, }?: {
     env?: NodeJS.ProcessEnv;
     cwd?: string;
+    preserveExistingKeys?: Iterable<string>;
 }): LoadedCopilotHubEnvironment;

package/packages/core/dist/env-config.js

@@ -3,7 +3,7 @@ import path from "node:path";
 import process from "node:process";
 import dotenv from "dotenv";
 import { resolveConfigBaseDir } from "./config-paths.js";
-export function loadCopilotHubEnvironment({ env = process.env, cwd = process.cwd(), } = {}) {
+export function loadCopilotHubEnvironment({ env = process.env, cwd = process.cwd(), preserveExistingKeys = [], } = {}) {
     const configuredEnvPath = String(env.COPILOT_HUB_ENV_PATH ?? "").trim();
     const resolvedEnvPath = configuredEnvPath ? path.resolve(configuredEnvPath) : "";
     const discoveredEnvPath = resolvedEnvPath || resolveDefaultEnvPath(cwd);
@@ -13,7 +13,7 @@ export function loadCopilotHubEnvironment({ env = process.env, cwd = process.cwd
         cwd,
     });
     const fileValues = loadEnvFileValues(discoveredEnvPath);
-    const overriddenKeys = applyEnvFileValues(env, fileValues);
+    const overriddenKeys = applyEnvFileValues(env, fileValues, preserveExistingKeys);
     if (resolvedEnvPath) {
         env.COPILOT_HUB_ENV_PATH = resolvedEnvPath;
     }
@@ -41,10 +41,14 @@ function loadEnvFileValues(filePath) {
         return {};
     }
 }
-function applyEnvFileValues(env, fileValues) {
+function applyEnvFileValues(env, fileValues, preserveExistingKeys) {
     const overriddenKeys = [];
+    const preservedKeys = new Set([...preserveExistingKeys].map((key) => String(key ?? "").trim()).filter(Boolean));
     for (const [key, value] of Object.entries(fileValues)) {
         const previousValue = String(env[key] ?? "");
+        if (previousValue && preservedKeys.has(key)) {
+            continue;
+        }
         if (previousValue && previousValue !== value) {
             overriddenKeys.push(key);
         }

package/packages/core/dist/env-config.js.map

@@ -1 +1 @@
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package/scripts/dist/cli.mjs

@@ -7,7 +7,7 @@ import { createInterface } from "node:readline/promises";
 import { fileURLToPath } from "node:url";
 import { spawnCodexSync } from "./codex-spawn.mjs";
 import { codexInstallPackageSpec } from "./codex-version.mjs";
-import { initializeCopilotHubLayout, resolveCopilotHubLayout } from "./install-layout.mjs";
+import { initializeCopilotHubLayout, resetCopilotHubConfig, resolveCopilotHubLayout, } from "./install-layout.mjs";
 import { buildCodexCompatibilityError, buildCodexCompatibilityNotice, probeCodexVersion, resolveCodexBinForStart, resolveCompatibleInstalledCodexBin, } from "./codex-runtime.mjs";
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -27,6 +27,7 @@ const rawArgs = process.argv
     .filter(Boolean);
 const wantsVersion = rawArgs.includes("--version") || rawArgs.includes("-v");
 const wantsHelp = rawArgs.includes("--help") || rawArgs.includes("-h");
+const wantsYes = rawArgs.includes("--yes") || rawArgs.includes("-y");
 const action = String(rawArgs[0] ?? "start")
     .trim()
     .toLowerCase();
@@ -92,6 +93,13 @@ async function main() {
             runNode(["scripts/dist/configure.mjs"]);
             return;
         }
+        case "reset-config":
+        case "reset_config": {
+            await resetConfig({
+                force: wantsYes,
+            });
+            return;
+        }
         case "service": {
             const serviceAction = String(rawArgs[1] ?? "")
                 .trim()
@@ -111,6 +119,47 @@ async function main() {
         }
     }
 }
+async function resetConfig({ force }) {
+    if (!force) {
+        if (!process.stdin.isTTY) {
+            throw new Error("reset-config requires confirmation. Re-run with '--yes' in non-interactive mode.");
+        }
+        const rl = createInterface({ input, output });
+        try {
+            const confirmed = await askYesNo(rl, [
+                "Reset Copilot Hub config and runtime state?",
+                "This removes persisted config, bot registry, secrets, logs, and runtime state.",
+                "Agent workspaces are kept.",
+            ].join(" "), false);
+            if (!confirmed) {
+                console.log("Reset canceled.");
+                return;
+            }
+        }
+        finally {
+            rl.close();
+        }
+    }
+    if (isServiceAlreadyInstalled()) {
+        runNodeCapture(["scripts/dist/service.mjs", "stop"], "inherit");
+    }
+    else {
+        runNodeCapture(["scripts/dist/supervisor.mjs", "down"], "inherit");
+    }
+    const reset = resetCopilotHubConfig({ layout });
+    initializeCopilotHubLayout({ repoRoot, layout });
+    console.log("Copilot Hub config reset completed.");
+    if (reset.removedPaths.length > 0) {
+        console.log("Removed:");
+        for (const removedPath of reset.removedPaths) {
+            console.log(`- ${removedPath}`);
+        }
+    }
+    console.log("Kept:");
+    console.log("- package installation");
+    console.log("- external workspaces (for example Desktop/copilot_workspaces)");
+    console.log("Next step: run 'copilot-hub configure' then 'copilot-hub start'.");
+}
 function runNode(scriptArgs) {
     const result = runNodeCapture(scriptArgs, "inherit");
     const code = Number.isInteger(result.status) ? result.status : 1;
@@ -485,6 +534,8 @@ function spawnNpm(args, options) {
 function printUsage() {
     console.log([
         "Usage: node scripts/dist/cli.mjs <start|stop|restart|status|logs|configure|service|version|help>",
+        "Reset persistent state:",
+        "  node scripts/dist/cli.mjs reset-config [--yes]",
         "Service management:",
         "  node scripts/dist/cli.mjs service <install|uninstall|status|start|stop|help>",
     ].join("\n"));

package/scripts/dist/configure.mjs

@@ -4,6 +4,7 @@ import path from "node:path";
 import process, { stdin as input, stdout as output } from "node:process";
 import { fileURLToPath } from "node:url";
 import { createInterface } from "node:readline/promises";
+import { parseEnvMap, readEnvLines, setEnvValue, writeEnvLines } from "./env-file-utils.mjs";
 import { initializeCopilotHubLayout, resolveCopilotHubLayout } from "./install-layout.mjs";
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -23,8 +24,8 @@ await main();
 async function main() {
     ensureEnvFile(engineEnvPath, engineExamplePath);
     ensureEnvFile(controlPlaneEnvPath, controlPlaneExamplePath);
-    const engineLines = readLines(engineEnvPath);
-    const controlPlaneLines = readLines(controlPlaneEnvPath);
+    const engineLines = readEnvLines(engineEnvPath);
+    const controlPlaneLines = readEnvLines(controlPlaneEnvPath);
     const rl = createInterface({ input, output });
     try {
         if (requiredOnly) {
@@ -41,8 +42,8 @@ async function main() {
     finally {
         rl.close();
     }
-    writeLines(engineEnvPath, engineLines);
-    writeLines(controlPlaneEnvPath, controlPlaneLines);
+    writeEnvLines(engineEnvPath, engineLines);
+    writeEnvLines(controlPlaneEnvPath, controlPlaneLines);
 }
 async function configureRequiredTokens({ rl, controlPlaneLines }) {
     const controlPlaneTokenEnvName = migrateControlPlaneTokenEnv(controlPlaneLines);
@@ -102,67 +103,10 @@ function ensureEnvFile(envPath, examplePath) {
     }
     fs.writeFileSync(envPath, "", "utf8");
 }
-function readLines(filePath) {
-    const content = fs.readFileSync(filePath, "utf8");
-    return content.split(/\r?\n/);
-}
-function writeLines(filePath, lines) {
-    const normalized = [...lines];
-    if (normalized.length === 0 || normalized[normalized.length - 1] !== "") {
-        normalized.push("");
-    }
-    fs.writeFileSync(filePath, normalized.join("\n"), "utf8");
-}
-function parseEnvMap(lines) {
-    const map = {};
-    for (const line of lines) {
-        const match = line.match(/^\s*([A-Za-z_][A-Za-z0-9_]*)\s*=\s*(.*)\s*$/);
-        if (!match) {
-            continue;
-        }
-        const key = match[1];
-        const value = unquote(match[2] ?? "");
-        map[key] = value;
-    }
-    return map;
-}
-function setEnvValue(lines, key, value) {
-    const safeValue = sanitizeValue(value);
-    const pattern = new RegExp(`^\\s*${escapeRegex(key)}\\s*=`);
-    for (let index = 0; index < lines.length; index += 1) {
-        if (!pattern.test(lines[index])) {
-            continue;
-        }
-        lines[index] = `${key}=${safeValue}`;
-        return;
-    }
-    if (lines.length > 0 && lines[lines.length - 1] !== "") {
-        lines.push("");
-    }
-    lines.push(`${key}=${safeValue}`);
-}
-function sanitizeValue(value) {
-    return String(value ?? "")
-        .replace(/[\r\n]/g, "")
-        .trim();
-}
-function unquote(value) {
-    const raw = String(value ?? "").trim();
-    if (!raw) {
-        return "";
-    }
-    if ((raw.startsWith('"') && raw.endsWith('"')) || (raw.startsWith("'") && raw.endsWith("'"))) {
-        return raw.slice(1, -1);
-    }
-    return raw;
-}
 function nonEmpty(value, fallback) {
     const normalized = String(value ?? "").trim();
     return normalized || fallback;
 }
-function escapeRegex(value) {
-    return String(value).replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-}
 async function askRequired(rl, label) {
     while (true) {
         const value = await rl.question(`${label}: `);

package/scripts/dist/env-file-utils.mjs

@@ -0,0 +1,83 @@
+import fs from "node:fs";
+export function ensureEnvTextFile(filePath) {
+    if (fs.existsSync(filePath)) {
+        return;
+    }
+    fs.mkdirSync(requireParentDir(filePath), { recursive: true });
+    fs.writeFileSync(filePath, "", "utf8");
+}
+export function readEnvLines(filePath) {
+    const content = fs.readFileSync(filePath, "utf8");
+    return content.split(/\r?\n/);
+}
+export function writeEnvLines(filePath, lines) {
+    const normalized = [...lines];
+    if (normalized.length === 0 || normalized[normalized.length - 1] !== "") {
+        normalized.push("");
+    }
+    fs.writeFileSync(filePath, normalized.join("\n"), "utf8");
+}
+export function parseEnvMap(lines) {
+    const map = {};
+    for (const line of lines) {
+        const match = line.match(/^\s*([A-Za-z_][A-Za-z0-9_]*)\s*=\s*(.*)\s*$/);
+        if (!match) {
+            continue;
+        }
+        const key = match[1];
+        const value = unquote(match[2] ?? "");
+        map[key] = value;
+    }
+    return map;
+}
+export function setEnvValue(lines, key, value) {
+    const safeValue = sanitizeEnvValue(value);
+    const pattern = new RegExp(`^\\s*${escapeRegex(key)}\\s*=`);
+    for (let index = 0; index < lines.length; index += 1) {
+        if (!pattern.test(lines[index])) {
+            continue;
+        }
+        lines[index] = `${key}=${safeValue}`;
+        return;
+    }
+    if (lines.length > 0 && lines[lines.length - 1] !== "") {
+        lines.push("");
+    }
+    lines.push(`${key}=${safeValue}`);
+}
+export function removeEnvKeys(lines, keys) {
+    const patterns = keys.map((key) => new RegExp(`^\\s*${escapeRegex(key)}\\s*=`));
+    const originalLength = lines.length;
+    const kept = lines.filter((line) => !patterns.some((pattern) => pattern.test(line)));
+    if (kept.length === originalLength) {
+        return false;
+    }
+    lines.splice(0, lines.length, ...kept);
+    return true;
+}
+export function sanitizeEnvValue(value) {
+    return String(value ?? "")
+        .replace(/[\r\n]/g, "")
+        .trim();
+}
+function unquote(value) {
+    const raw = String(value ?? "").trim();
+    if (!raw) {
+        return "";
+    }
+    if ((raw.startsWith('"') && raw.endsWith('"')) || (raw.startsWith("'") && raw.endsWith("'"))) {
+        return raw.slice(1, -1);
+    }
+    return raw;
+}
+function escapeRegex(value) {
+    return String(value).replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
+function requireParentDir(filePath) {
+    const parts = String(filePath ?? "").split(/[\\/]/);
+    if (parts.length <= 1) {
+        return ".";
+    }
+    parts.pop();
+    return parts.join("/") || ".";
+}

package/scripts/dist/install-layout.mjs

@@ -2,6 +2,8 @@
 import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
+import process from "node:process";
+import { parseEnvMap, readEnvLines, removeEnvKeys, writeEnvLines } from "./env-file-utils.mjs";
 export function resolveCopilotHubLayout({ repoRoot, env = process.env, platform = process.platform, homeDirectory = os.homedir(), }) {
     const pathApi = getPathApi(platform);
     const homeDir = resolveCopilotHubHomeDir({
@@ -30,7 +32,35 @@ export function resolveCopilotHubLayout({ repoRoot, env = process.env, platform
 export function initializeCopilotHubLayout({ repoRoot, layout, }) {
     ensureCopilotHubLayout(layout);
     const migratedPaths = migrateLegacyLayout({ repoRoot, layout });
-    return { migratedPaths };
+    const normalizedEnvPaths = normalizePersistentEnvFiles(layout);
+    return { migratedPaths, normalizedEnvPaths };
+}
+export function resetCopilotHubConfig({ layout }) {
+    const removedPaths = [];
+    for (const target of [layout.configDir, layout.dataDir, layout.logsDir]) {
+        if (!fs.existsSync(target)) {
+            continue;
+        }
+        fs.rmSync(target, { recursive: true, force: true });
+        removedPaths.push(target);
+    }
+    const runtimeTargets = [
+        path.join(layout.runtimeDir, "pids"),
+        path.join(layout.runtimeDir, "services"),
+        path.join(layout.runtimeDir, "last-startup-error.json"),
+        layout.servicePromptStatePath,
+    ];
+    for (const target of runtimeTargets) {
+        if (!fs.existsSync(target)) {
+            continue;
+        }
+        fs.rmSync(target, { recursive: true, force: true });
+        removedPaths.push(target);
+    }
+    ensureCopilotHubLayout(layout);
+    return {
+        removedPaths: removedPaths.sort(),
+    };
 }
 export function ensureCopilotHubLayout(layout) {
     fs.mkdirSync(layout.homeDir, { recursive: true });
@@ -81,6 +111,98 @@ function migrateLegacyLayout({ repoRoot, layout, }) {
     }
     return migratedPaths;
 }
+function normalizePersistentEnvFiles(layout) {
+    const normalizedPaths = [];
+    if (normalizePersistentEnvFile(layout.agentEngineEnvPath, [
+        {
+            key: "BOT_DATA_DIR",
+            legacyValues: ["./data"],
+            wrongResolvedPath: path.join(layout.configDir, "data"),
+        },
+        {
+            key: "BOT_REGISTRY_FILE",
+            legacyValues: ["./data/bot-registry.json"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "bot-registry.json"),
+        },
+        {
+            key: "SECRET_STORE_FILE",
+            legacyValues: ["./data/secrets.json"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "secrets.json"),
+        },
+        {
+            key: "INSTANCE_LOCK_FILE",
+            legacyValues: ["./data/runtime.lock"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "runtime.lock"),
+        },
+    ])) {
+        normalizedPaths.push(layout.agentEngineEnvPath);
+    }
+    if (normalizePersistentEnvFile(layout.controlPlaneEnvPath, [
+        {
+            key: "BOT_DATA_DIR",
+            legacyValues: ["./data"],
+            wrongResolvedPath: path.join(layout.configDir, "data"),
+        },
+        {
+            key: "BOT_REGISTRY_FILE",
+            legacyValues: ["./data/bot-registry.json"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "bot-registry.json"),
+        },
+        {
+            key: "SECRET_STORE_FILE",
+            legacyValues: ["./data/secrets.json"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "secrets.json"),
+        },
+        {
+            key: "INSTANCE_LOCK_FILE",
+            legacyValues: ["./data/runtime.lock"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "runtime.lock"),
+        },
+        {
+            key: "HUB_DATA_DIR",
+            legacyValues: ["./data/copilot_hub"],
+            wrongResolvedPath: path.join(layout.configDir, "data", "copilot_hub"),
+        },
+    ])) {
+        normalizedPaths.push(layout.controlPlaneEnvPath);
+    }
+    return normalizedPaths.sort();
+}
+function normalizePersistentEnvFile(filePath, rules) {
+    if (!fs.existsSync(filePath)) {
+        return false;
+    }
+    const lines = readEnvLines(filePath);
+    const envMap = parseEnvMap(lines);
+    const keysToRemove = rules
+        .filter((rule) => shouldRemoveLegacyManagedPath(envMap[rule.key], {
+        legacyValues: rule.legacyValues,
+        wrongResolvedPath: rule.wrongResolvedPath,
+        configBaseDir: path.dirname(filePath),
+    }))
+        .map((rule) => rule.key);
+    if (keysToRemove.length === 0) {
+        return false;
+    }
+    removeEnvKeys(lines, keysToRemove);
+    writeEnvLines(filePath, lines);
+    return true;
+}
+function shouldRemoveLegacyManagedPath(rawValue, { legacyValues, wrongResolvedPath, configBaseDir, }) {
+    const value = String(rawValue ?? "").trim();
+    if (!value) {
+        return false;
+    }
+    const normalizedValue = normalizeForCompare(value);
+    if (legacyValues.some((entry) => normalizeForCompare(entry) === normalizedValue)) {
+        return true;
+    }
+    if (path.isAbsolute(value)) {
+        return normalizeForCompare(value) === normalizeForCompare(wrongResolvedPath);
+    }
+    return (normalizeForCompare(path.resolve(configBaseDir, value)) ===
+        normalizeForCompare(wrongResolvedPath));
+}
 function resolveLegacyPaths(repoRoot) {
     return {
         agentEngineEnvPath: path.join(repoRoot, "apps", "agent-engine", ".env"),
@@ -129,6 +251,13 @@ function normalizePath(value, pathApi) {
     const normalized = String(value ?? "").trim();
     return normalized ? pathApi.resolve(normalized) : "";
 }
+function normalizeForCompare(value) {
+    const normalized = String(value ?? "").trim();
+    if (!normalized) {
+        return "";
+    }
+    return process.platform === "win32" ? normalized.toLowerCase() : normalized;
+}
 function getPathApi(platform) {
     return platform === "win32" ? path.win32 : path.posix;
 }

package/scripts/dist/supervisor.mjs

@@ -307,6 +307,11 @@ function buildServiceEnvironment(service) {
         BOT_REGISTRY_FILE: service.botRegistryFilePath,
         SECRET_STORE_FILE: service.secretStoreFilePath,
         INSTANCE_LOCK_FILE: service.instanceLockFilePath,
+        ...(service.id === "control-plane"
+            ? {
+                HUB_DATA_DIR: path.join(service.dataDir, "copilot_hub"),
+            }
+            : {}),
     };
 }
 function printTail(filePath, lines) {

package/scripts/src/cli.mts

@@ -7,7 +7,11 @@ import { createInterface } from "node:readline/promises";
 import { fileURLToPath } from "node:url";
 import { spawnCodexSync } from "./codex-spawn.mjs";
 import { codexInstallPackageSpec } from "./codex-version.mjs";
-import { initializeCopilotHubLayout, resolveCopilotHubLayout } from "./install-layout.mjs";
+import {
+  initializeCopilotHubLayout,
+  resetCopilotHubConfig,
+  resolveCopilotHubLayout,
+} from "./install-layout.mjs";
 import {
   buildCodexCompatibilityError,
   buildCodexCompatibilityNotice,
@@ -35,6 +39,7 @@ const rawArgs = process.argv
   .filter(Boolean);
 const wantsVersion = rawArgs.includes("--version") || rawArgs.includes("-v");
 const wantsHelp = rawArgs.includes("--help") || rawArgs.includes("-h");
+const wantsYes = rawArgs.includes("--yes") || rawArgs.includes("-y");
 
 const action = String(rawArgs[0] ?? "start")
   .trim()
@@ -106,6 +111,13 @@ async function main() {
       runNode(["scripts/dist/configure.mjs"]);
       return;
     }
+    case "reset-config":
+    case "reset_config": {
+      await resetConfig({
+        force: wantsYes,
+      });
+      return;
+    }
     case "service": {
       const serviceAction = String(rawArgs[1] ?? "")
         .trim()
@@ -126,6 +138,56 @@ async function main() {
   }
 }
 
+async function resetConfig({ force }: { force: boolean }): Promise<void> {
+  if (!force) {
+    if (!process.stdin.isTTY) {
+      throw new Error(
+        "reset-config requires confirmation. Re-run with '--yes' in non-interactive mode.",
+      );
+    }
+
+    const rl = createInterface({ input, output });
+    try {
+      const confirmed = await askYesNo(
+        rl,
+        [
+          "Reset Copilot Hub config and runtime state?",
+          "This removes persisted config, bot registry, secrets, logs, and runtime state.",
+          "Agent workspaces are kept.",
+        ].join(" "),
+        false,
+      );
+      if (!confirmed) {
+        console.log("Reset canceled.");
+        return;
+      }
+    } finally {
+      rl.close();
+    }
+  }
+
+  if (isServiceAlreadyInstalled()) {
+    runNodeCapture(["scripts/dist/service.mjs", "stop"], "inherit");
+  } else {
+    runNodeCapture(["scripts/dist/supervisor.mjs", "down"], "inherit");
+  }
+
+  const reset = resetCopilotHubConfig({ layout });
+  initializeCopilotHubLayout({ repoRoot, layout });
+
+  console.log("Copilot Hub config reset completed.");
+  if (reset.removedPaths.length > 0) {
+    console.log("Removed:");
+    for (const removedPath of reset.removedPaths) {
+      console.log(`- ${removedPath}`);
+    }
+  }
+  console.log("Kept:");
+  console.log("- package installation");
+  console.log("- external workspaces (for example Desktop/copilot_workspaces)");
+  console.log("Next step: run 'copilot-hub configure' then 'copilot-hub start'.");
+}
+
 function runNode(scriptArgs) {
   const result = runNodeCapture(scriptArgs, "inherit");
   const code = Number.isInteger(result.status) ? result.status : 1;
@@ -577,6 +639,8 @@ function printUsage() {
   console.log(
     [
       "Usage: node scripts/dist/cli.mjs <start|stop|restart|status|logs|configure|service|version|help>",
+      "Reset persistent state:",
+      "  node scripts/dist/cli.mjs reset-config [--yes]",
       "Service management:",
       "  node scripts/dist/cli.mjs service <install|uninstall|status|start|stop|help>",
     ].join("\n"),

package/scripts/src/configure.mts

@@ -4,6 +4,7 @@ import path from "node:path";
 import process, { stdin as input, stdout as output } from "node:process";
 import { fileURLToPath } from "node:url";
 import { createInterface } from "node:readline/promises";
+import { parseEnvMap, readEnvLines, setEnvValue, writeEnvLines } from "./env-file-utils.mjs";
 import { initializeCopilotHubLayout, resolveCopilotHubLayout } from "./install-layout.mjs";
 
 const __filename = fileURLToPath(import.meta.url);
@@ -30,8 +31,8 @@ async function main() {
   ensureEnvFile(engineEnvPath, engineExamplePath);
   ensureEnvFile(controlPlaneEnvPath, controlPlaneExamplePath);
 
-  const engineLines = readLines(engineEnvPath);
-  const controlPlaneLines = readLines(controlPlaneEnvPath);
+  const engineLines = readEnvLines(engineEnvPath);
+  const controlPlaneLines = readEnvLines(controlPlaneEnvPath);
 
   const rl = createInterface({ input, output });
 
@@ -49,8 +50,8 @@ async function main() {
     rl.close();
   }
 
-  writeLines(engineEnvPath, engineLines);
-  writeLines(controlPlaneEnvPath, controlPlaneLines);
+  writeEnvLines(engineEnvPath, engineLines);
+  writeEnvLines(controlPlaneEnvPath, controlPlaneLines);
 }
 
 async function configureRequiredTokens({ rl, controlPlaneLines }) {
@@ -132,80 +133,11 @@ function ensureEnvFile(envPath, examplePath) {
   fs.writeFileSync(envPath, "", "utf8");
 }
 
-function readLines(filePath) {
-  const content = fs.readFileSync(filePath, "utf8");
-  return content.split(/\r?\n/);
-}
-
-function writeLines(filePath, lines) {
-  const normalized = [...lines];
-  if (normalized.length === 0 || normalized[normalized.length - 1] !== "") {
-    normalized.push("");
-  }
-  fs.writeFileSync(filePath, normalized.join("\n"), "utf8");
-}
-
-function parseEnvMap(lines) {
-  const map: Record<string, string> = {};
-  for (const line of lines) {
-    const match = line.match(/^\s*([A-Za-z_][A-Za-z0-9_]*)\s*=\s*(.*)\s*$/);
-    if (!match) {
-      continue;
-    }
-
-    const key = match[1];
-    const value = unquote(match[2] ?? "");
-    map[key] = value;
-  }
-  return map;
-}
-
-function setEnvValue(lines, key, value) {
-  const safeValue = sanitizeValue(value);
-  const pattern = new RegExp(`^\\s*${escapeRegex(key)}\\s*=`);
-  for (let index = 0; index < lines.length; index += 1) {
-    if (!pattern.test(lines[index])) {
-      continue;
-    }
-
-    lines[index] = `${key}=${safeValue}`;
-    return;
-  }
-
-  if (lines.length > 0 && lines[lines.length - 1] !== "") {
-    lines.push("");
-  }
-  lines.push(`${key}=${safeValue}`);
-}
-
-function sanitizeValue(value) {
-  return String(value ?? "")
-    .replace(/[\r\n]/g, "")
-    .trim();
-}
-
-function unquote(value) {
-  const raw = String(value ?? "").trim();
-  if (!raw) {
-    return "";
-  }
-
-  if ((raw.startsWith('"') && raw.endsWith('"')) || (raw.startsWith("'") && raw.endsWith("'"))) {
-    return raw.slice(1, -1);
-  }
-
-  return raw;
-}
-
 function nonEmpty(value, fallback) {
   const normalized = String(value ?? "").trim();
   return normalized || fallback;
 }
 
-function escapeRegex(value) {
-  return String(value).replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-}
-
 async function askRequired(rl, label) {
   while (true) {
     const value = await rl.question(`${label}: `);

package/scripts/src/env-file-utils.mts

@@ -0,0 +1,98 @@
+import fs from "node:fs";
+
+export function ensureEnvTextFile(filePath: string): void {
+  if (fs.existsSync(filePath)) {
+    return;
+  }
+  fs.mkdirSync(requireParentDir(filePath), { recursive: true });
+  fs.writeFileSync(filePath, "", "utf8");
+}
+
+export function readEnvLines(filePath: string): string[] {
+  const content = fs.readFileSync(filePath, "utf8");
+  return content.split(/\r?\n/);
+}
+
+export function writeEnvLines(filePath: string, lines: string[]): void {
+  const normalized = [...lines];
+  if (normalized.length === 0 || normalized[normalized.length - 1] !== "") {
+    normalized.push("");
+  }
+  fs.writeFileSync(filePath, normalized.join("\n"), "utf8");
+}
+
+export function parseEnvMap(lines: string[]): Record<string, string> {
+  const map: Record<string, string> = {};
+  for (const line of lines) {
+    const match = line.match(/^\s*([A-Za-z_][A-Za-z0-9_]*)\s*=\s*(.*)\s*$/);
+    if (!match) {
+      continue;
+    }
+
+    const key = match[1];
+    const value = unquote(match[2] ?? "");
+    map[key] = value;
+  }
+  return map;
+}
+
+export function setEnvValue(lines: string[], key: string, value: unknown): void {
+  const safeValue = sanitizeEnvValue(value);
+  const pattern = new RegExp(`^\\s*${escapeRegex(key)}\\s*=`);
+  for (let index = 0; index < lines.length; index += 1) {
+    if (!pattern.test(lines[index])) {
+      continue;
+    }
+
+    lines[index] = `${key}=${safeValue}`;
+    return;
+  }
+
+  if (lines.length > 0 && lines[lines.length - 1] !== "") {
+    lines.push("");
+  }
+  lines.push(`${key}=${safeValue}`);
+}
+
+export function removeEnvKeys(lines: string[], keys: readonly string[]): boolean {
+  const patterns = keys.map((key) => new RegExp(`^\\s*${escapeRegex(key)}\\s*=`));
+  const originalLength = lines.length;
+  const kept = lines.filter((line) => !patterns.some((pattern) => pattern.test(line)));
+  if (kept.length === originalLength) {
+    return false;
+  }
+  lines.splice(0, lines.length, ...kept);
+  return true;
+}
+
+export function sanitizeEnvValue(value: unknown): string {
+  return String(value ?? "")
+    .replace(/[\r\n]/g, "")
+    .trim();
+}
+
+function unquote(value: string): string {
+  const raw = String(value ?? "").trim();
+  if (!raw) {
+    return "";
+  }
+
+  if ((raw.startsWith('"') && raw.endsWith('"')) || (raw.startsWith("'") && raw.endsWith("'"))) {
+    return raw.slice(1, -1);
+  }
+
+  return raw;
+}
+
+function escapeRegex(value: string): string {
+  return String(value).replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
+
+function requireParentDir(filePath: string): string {
+  const parts = String(filePath ?? "").split(/[\\/]/);
+  if (parts.length <= 1) {
+    return ".";
+  }
+  parts.pop();
+  return parts.join("/") || ".";
+}

package/scripts/src/install-layout.mts

@@ -2,6 +2,8 @@
 import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
+import process from "node:process";
+import { parseEnvMap, readEnvLines, removeEnvKeys, writeEnvLines } from "./env-file-utils.mjs";
 
 export type CopilotHubLayout = {
   homeDir: string;
@@ -60,10 +62,44 @@ export function initializeCopilotHubLayout({
 }: {
   repoRoot: string;
   layout: CopilotHubLayout;
-}): { migratedPaths: string[] } {
+}): { migratedPaths: string[]; normalizedEnvPaths: string[] } {
   ensureCopilotHubLayout(layout);
   const migratedPaths = migrateLegacyLayout({ repoRoot, layout });
-  return { migratedPaths };
+  const normalizedEnvPaths = normalizePersistentEnvFiles(layout);
+  return { migratedPaths, normalizedEnvPaths };
+}
+
+export function resetCopilotHubConfig({ layout }: { layout: CopilotHubLayout }): {
+  removedPaths: string[];
+} {
+  const removedPaths: string[] = [];
+
+  for (const target of [layout.configDir, layout.dataDir, layout.logsDir]) {
+    if (!fs.existsSync(target)) {
+      continue;
+    }
+    fs.rmSync(target, { recursive: true, force: true });
+    removedPaths.push(target);
+  }
+
+  const runtimeTargets = [
+    path.join(layout.runtimeDir, "pids"),
+    path.join(layout.runtimeDir, "services"),
+    path.join(layout.runtimeDir, "last-startup-error.json"),
+    layout.servicePromptStatePath,
+  ];
+  for (const target of runtimeTargets) {
+    if (!fs.existsSync(target)) {
+      continue;
+    }
+    fs.rmSync(target, { recursive: true, force: true });
+    removedPaths.push(target);
+  }
+
+  ensureCopilotHubLayout(layout);
+  return {
+    removedPaths: removedPaths.sort(),
+  };
 }
 
 export function ensureCopilotHubLayout(layout: CopilotHubLayout): void {
@@ -137,6 +173,132 @@ function migrateLegacyLayout({
   return migratedPaths;
 }
 
+function normalizePersistentEnvFiles(layout: CopilotHubLayout): string[] {
+  const normalizedPaths: string[] = [];
+
+  if (
+    normalizePersistentEnvFile(layout.agentEngineEnvPath, [
+      {
+        key: "BOT_DATA_DIR",
+        legacyValues: ["./data"],
+        wrongResolvedPath: path.join(layout.configDir, "data"),
+      },
+      {
+        key: "BOT_REGISTRY_FILE",
+        legacyValues: ["./data/bot-registry.json"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "bot-registry.json"),
+      },
+      {
+        key: "SECRET_STORE_FILE",
+        legacyValues: ["./data/secrets.json"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "secrets.json"),
+      },
+      {
+        key: "INSTANCE_LOCK_FILE",
+        legacyValues: ["./data/runtime.lock"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "runtime.lock"),
+      },
+    ])
+  ) {
+    normalizedPaths.push(layout.agentEngineEnvPath);
+  }
+
+  if (
+    normalizePersistentEnvFile(layout.controlPlaneEnvPath, [
+      {
+        key: "BOT_DATA_DIR",
+        legacyValues: ["./data"],
+        wrongResolvedPath: path.join(layout.configDir, "data"),
+      },
+      {
+        key: "BOT_REGISTRY_FILE",
+        legacyValues: ["./data/bot-registry.json"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "bot-registry.json"),
+      },
+      {
+        key: "SECRET_STORE_FILE",
+        legacyValues: ["./data/secrets.json"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "secrets.json"),
+      },
+      {
+        key: "INSTANCE_LOCK_FILE",
+        legacyValues: ["./data/runtime.lock"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "runtime.lock"),
+      },
+      {
+        key: "HUB_DATA_DIR",
+        legacyValues: ["./data/copilot_hub"],
+        wrongResolvedPath: path.join(layout.configDir, "data", "copilot_hub"),
+      },
+    ])
+  ) {
+    normalizedPaths.push(layout.controlPlaneEnvPath);
+  }
+
+  return normalizedPaths.sort();
+}
+
+function normalizePersistentEnvFile(
+  filePath: string,
+  rules: Array<{ key: string; legacyValues: string[]; wrongResolvedPath: string }>,
+): boolean {
+  if (!fs.existsSync(filePath)) {
+    return false;
+  }
+
+  const lines = readEnvLines(filePath);
+  const envMap = parseEnvMap(lines);
+  const keysToRemove = rules
+    .filter((rule) =>
+      shouldRemoveLegacyManagedPath(envMap[rule.key], {
+        legacyValues: rule.legacyValues,
+        wrongResolvedPath: rule.wrongResolvedPath,
+        configBaseDir: path.dirname(filePath),
+      }),
+    )
+    .map((rule) => rule.key);
+
+  if (keysToRemove.length === 0) {
+    return false;
+  }
+
+  removeEnvKeys(lines, keysToRemove);
+  writeEnvLines(filePath, lines);
+  return true;
+}
+
+function shouldRemoveLegacyManagedPath(
+  rawValue: string | undefined,
+  {
+    legacyValues,
+    wrongResolvedPath,
+    configBaseDir,
+  }: {
+    legacyValues: string[];
+    wrongResolvedPath: string;
+    configBaseDir: string;
+  },
+): boolean {
+  const value = String(rawValue ?? "").trim();
+  if (!value) {
+    return false;
+  }
+
+  const normalizedValue = normalizeForCompare(value);
+  if (legacyValues.some((entry) => normalizeForCompare(entry) === normalizedValue)) {
+    return true;
+  }
+
+  if (path.isAbsolute(value)) {
+    return normalizeForCompare(value) === normalizeForCompare(wrongResolvedPath);
+  }
+
+  return (
+    normalizeForCompare(path.resolve(configBaseDir, value)) ===
+    normalizeForCompare(wrongResolvedPath)
+  );
+}
+
 function resolveLegacyPaths(repoRoot: string): {
   agentEngineEnvPath: string;
   controlPlaneEnvPath: string;
@@ -195,6 +357,14 @@ function normalizePath(value: unknown, pathApi: typeof path.posix | typeof path.
   return normalized ? pathApi.resolve(normalized) : "";
 }
 
+function normalizeForCompare(value: unknown): string {
+  const normalized = String(value ?? "").trim();
+  if (!normalized) {
+    return "";
+  }
+  return process.platform === "win32" ? normalized.toLowerCase() : normalized;
+}
+
 function getPathApi(platform: NodeJS.Platform): typeof path.posix | typeof path.win32 {
   return platform === "win32" ? path.win32 : path.posix;
 }

package/scripts/src/supervisor.mts

@@ -354,6 +354,11 @@ function buildServiceEnvironment(service) {
     BOT_REGISTRY_FILE: service.botRegistryFilePath,
     SECRET_STORE_FILE: service.secretStoreFilePath,
     INSTANCE_LOCK_FILE: service.instanceLockFilePath,
+    ...(service.id === "control-plane"
+      ? {
+          HUB_DATA_DIR: path.join(service.dataDir, "copilot_hub"),
+        }
+      : {}),
   };
 }
 

package/scripts/test/install-layout.test.mjs

@@ -5,6 +5,7 @@ import path from "node:path";
 import test from "node:test";
 import {
   initializeCopilotHubLayout,
+  resetCopilotHubConfig,
   resolveCopilotHubHomeDir,
   resolveCopilotHubLayout,
 } from "../dist/install-layout.mjs";
@@ -45,8 +46,16 @@ test("initializeCopilotHubLayout migrates legacy env and data files once", () =>
   fs.mkdirSync(path.dirname(legacyControlEnvPath), { recursive: true });
   fs.mkdirSync(path.dirname(legacyEngineDataFile), { recursive: true });
   fs.mkdirSync(path.dirname(legacyPromptStatePath), { recursive: true });
-  fs.writeFileSync(legacyEngineEnvPath, "TELEGRAM_TOKEN_AGENT_1=123:abc\n", "utf8");
-  fs.writeFileSync(legacyControlEnvPath, "HUB_TELEGRAM_TOKEN=456:def\n", "utf8");
+  fs.writeFileSync(
+    legacyEngineEnvPath,
+    ["TELEGRAM_TOKEN_AGENT_1=123:abc", "BOT_REGISTRY_FILE=./data/bot-registry.json", ""].join("\n"),
+    "utf8",
+  );
+  fs.writeFileSync(
+    legacyControlEnvPath,
+    ["HUB_TELEGRAM_TOKEN=456:def", "HUB_DATA_DIR=./data/copilot_hub", ""].join("\n"),
+    "utf8",
+  );
   fs.writeFileSync(legacyEngineDataFile, '{"ok":true}\n', "utf8");
   fs.writeFileSync(legacyEngineLockPath, "stale-lock\n", "utf8");
   fs.writeFileSync(legacyPromptStatePath, '{"decision":"accepted"}\n', "utf8");
@@ -79,4 +88,47 @@ test("initializeCopilotHubLayout migrates legacy env and data files once", () =>
 
   const secondPass = initializeCopilotHubLayout({ repoRoot, layout });
   assert.deepEqual(secondPass.migratedPaths, []);
+  assert.deepEqual(secondPass.normalizedEnvPaths, []);
+});
+
+test("resetCopilotHubConfig removes persisted state but keeps the layout shell", () => {
+  const repoRoot = fs.mkdtempSync(path.join(os.tmpdir(), "copilot-hub-reset-"));
+  const layout = resolveCopilotHubLayout({
+    repoRoot,
+    env: {
+      COPILOT_HUB_HOME_DIR: path.join(repoRoot, "user-home"),
+    },
+    homeDirectory: repoRoot,
+  });
+
+  initializeCopilotHubLayout({ repoRoot, layout });
+  fs.writeFileSync(layout.agentEngineEnvPath, "TELEGRAM_TOKEN_AGENT_1=123:abc\n", "utf8");
+  fs.mkdirSync(layout.agentEngineDataDir, { recursive: true });
+  fs.writeFileSync(
+    path.join(layout.agentEngineDataDir, "bot-registry.json"),
+    '{"version":3}\n',
+    "utf8",
+  );
+  fs.mkdirSync(path.join(layout.runtimeDir, "pids"), { recursive: true });
+  fs.writeFileSync(path.join(layout.runtimeDir, "pids", "daemon.json"), '{"pid":1}\n', "utf8");
+  fs.writeFileSync(layout.servicePromptStatePath, '{"decision":"accepted"}\n', "utf8");
+  fs.writeFileSync(
+    path.join(layout.runtimeDir, "windows-daemon-launcher.vbs"),
+    "' launcher\n",
+    "utf8",
+  );
+
+  const reset = resetCopilotHubConfig({ layout });
+
+  assert.ok(reset.removedPaths.includes(layout.configDir));
+  assert.ok(reset.removedPaths.includes(layout.dataDir));
+  assert.ok(reset.removedPaths.includes(layout.logsDir));
+  assert.ok(fs.existsSync(layout.configDir));
+  assert.ok(fs.existsSync(layout.dataDir));
+  assert.ok(fs.existsSync(layout.logsDir));
+  assert.equal(fs.existsSync(layout.agentEngineEnvPath), false);
+  assert.equal(fs.existsSync(path.join(layout.agentEngineDataDir, "bot-registry.json")), false);
+  assert.equal(fs.existsSync(path.join(layout.runtimeDir, "pids")), false);
+  assert.equal(fs.existsSync(layout.servicePromptStatePath), false);
+  assert.equal(fs.existsSync(path.join(layout.runtimeDir, "windows-daemon-launcher.vbs")), true);
 });