@agentuity/cli 1.0.40 → 1.0.42

package/src/cmd/project/reconcile.ts

@@ -40,6 +40,14 @@ export interface ReconcileOptions {
 	interactive?: boolean;
 	/** If true, skip prompts and just validate */
 	validateOnly?: boolean;
+	/** If true, auto-confirm all prompts (--confirm flag) */
+	confirm?: boolean;
+	/** Pre-selected organization ID (skips org selection prompt) */
+	orgId?: string;
+	/** Pre-selected region (skips region selection prompt) */
+	region?: string;
+	/** Project name from --name flag */
+	name?: string;
 }
 
 /**
@@ -315,7 +323,7 @@ async function importExistingProject(
 ): Promise<ReconcileResult> {
 	const { dir, apiClient, config, logger } = opts;
 
-	if (!options?.skipPrompt) {
+	if (!options?.skipPrompt && opts.interactive !== false) {
 		tui.warning(
 			"You don't have access to this project. It may have been deleted or transferred to another organization."
 		);
@@ -333,29 +341,67 @@ async function importExistingProject(
 		tui.newline();
 	}
 
-	// Select org
-	const orgId = await selectOrg(orgs, config, existingConfig.orgId);
+	// Select org - use --org-id if provided, otherwise auto-select or prompt
+	let orgId: string;
+	if (opts.orgId) {
+		orgId = opts.orgId;
+	} else if (opts.confirm) {
+		orgId = await tui.selectOrganization(orgs, config.preferences?.orgId, true);
+	} else {
+		orgId = await selectOrg(orgs, config, existingConfig.orgId);
+	}
 
-	// Fetch regions and select
-	const regions = await tui.spinner({
-		message: 'Fetching regions',
-		clearOnSuccess: true,
-		callback: () => fetchRegionsWithCache(config.name, apiClient, logger),
-	});
-	const region = await selectRegion(regions, existingConfig.region);
+	// Select region (use pre-selected if available, otherwise fetch and prompt/auto-select)
+	let region: string;
+	if (opts.region) {
+		region = opts.region;
+	} else {
+		const regions = await tui.spinner({
+			message: 'Fetching regions',
+			clearOnSuccess: true,
+			callback: () => fetchRegionsWithCache(config.name, apiClient, logger),
+		});
+
+		if (opts.confirm) {
+			// Auto-select: use existing config region if valid, otherwise first available
+			const defaultRegion = existingConfig.region;
+			if (defaultRegion && regions.some((r) => r.region === defaultRegion)) {
+				region = defaultRegion;
+			} else {
+				const firstRegion = regions[0];
+				if (!firstRegion) {
+					return { status: 'error', message: 'No cloud regions available.' };
+				}
+				region = firstRegion.region;
+			}
+		} else {
+			region = await selectRegion(regions, existingConfig.region);
+		}
+	}
 
 	// Get project name
 	const defaultName = await getDefaultProjectName(dir);
-	const projectName = await textPrompt({
-		message: 'Project name:',
-		initial: defaultName,
-		validate: (value: string) => {
-			if (!value || value.trim().length === 0) {
-				return 'Project name is required';
-			}
-			return true;
-		},
-	});
+	let projectName: string;
+	if (opts.name) {
+		const trimmed = opts.name.trim();
+		if (trimmed.length === 0) {
+			return { status: 'error', message: 'Project name is required.' };
+		}
+		projectName = trimmed;
+	} else if (opts.confirm) {
+		projectName = defaultName;
+	} else {
+		projectName = await textPrompt({
+			message: 'Project name:',
+			initial: defaultName,
+			validate: (value: string) => {
+				if (!value || value.trim().length === 0) {
+					return 'Project name is required';
+				}
+				return true;
+			},
+		});
+	}
 
 	// Create the project
 	const newProject = await tui.spinner({
@@ -407,51 +453,87 @@ async function importExistingProject(
 async function createNewProject(opts: ReconcileOptions): Promise<ReconcileResult> {
 	const { dir, apiClient, config, logger } = opts;
 
-	tui.warning('This project is not registered with Agentuity Cloud.');
-	tui.newline();
+	if (opts.interactive !== false) {
+		tui.warning('This project is not registered with Agentuity Cloud.');
+		tui.newline();
+
+		const shouldCreate = await tui.confirm('Would you like to register it now?', true);
 
-	const shouldCreate = await tui.confirm('Would you like to register it now?', true);
+		if (!shouldCreate) {
+			return { status: 'skipped', message: 'Project registration cancelled.' };
+		}
 
-	if (!shouldCreate) {
-		return { status: 'skipped', message: 'Project registration cancelled.' };
+		tui.newline();
 	}
 
-	tui.newline();
-
-	// Fetch user's orgs
-	const orgs = await tui.spinner({
-		message: 'Fetching organizations',
-		clearOnSuccess: true,
-		callback: () => listOrganizations(apiClient),
-	});
+	// Select org - use --org-id if provided, otherwise fetch and select/auto-select
+	let orgId: string;
+	if (opts.orgId) {
+		orgId = opts.orgId;
+	} else {
+		// Fetch user's orgs
+		const orgs = await tui.spinner({
+			message: 'Fetching organizations',
+			clearOnSuccess: true,
+			callback: () => listOrganizations(apiClient),
+		});
+
+		if (orgs.length === 0) {
+			return { status: 'error', message: 'No organizations found for your account.' };
+		}
 
-	if (orgs.length === 0) {
-		return { status: 'error', message: 'No organizations found for your account.' };
+		if (opts.confirm) {
+			orgId = await tui.selectOrganization(orgs, config.preferences?.orgId, true);
+		} else {
+			orgId = await selectOrg(orgs, config);
+		}
 	}
 
-	// Select org
-	const orgId = await selectOrg(orgs, config);
-
-	// Fetch regions and select
-	const regions = await tui.spinner({
-		message: 'Fetching regions',
-		clearOnSuccess: true,
-		callback: () => fetchRegionsWithCache(config.name, apiClient, logger),
-	});
-	const region = await selectRegion(regions);
+	// Select region (use pre-selected if available, otherwise fetch and prompt/auto-select)
+	let region: string;
+	if (opts.region) {
+		region = opts.region;
+	} else {
+		const regions = await tui.spinner({
+			message: 'Fetching regions',
+			clearOnSuccess: true,
+			callback: () => fetchRegionsWithCache(config.name, apiClient, logger),
+		});
+
+		if (opts.confirm) {
+			const firstRegion = regions[0];
+			if (!firstRegion) {
+				return { status: 'error', message: 'No cloud regions available.' };
+			}
+			region = firstRegion.region;
+		} else {
+			region = await selectRegion(regions);
+		}
+	}
 
 	// Get project name from package.json or prompt
 	const defaultName = await getDefaultProjectName(dir);
-	const projectName = await textPrompt({
-		message: 'Project name:',
-		initial: defaultName,
-		validate: (value: string) => {
-			if (!value || value.trim().length === 0) {
-				return 'Project name is required';
-			}
-			return true;
-		},
-	});
+	let projectName: string;
+	if (opts.name) {
+		const trimmed = opts.name.trim();
+		if (trimmed.length === 0) {
+			return { status: 'error', message: 'Project name is required.' };
+		}
+		projectName = trimmed;
+	} else if (opts.confirm) {
+		projectName = defaultName;
+	} else {
+		projectName = await textPrompt({
+			message: 'Project name:',
+			initial: defaultName,
+			validate: (value: string) => {
+				if (!value || value.trim().length === 0) {
+					return 'Project name is required';
+				}
+				return true;
+			},
+		});
+	}
 
 	// Create the project
 	const newProject = await tui.spinner({
@@ -627,7 +709,7 @@ export async function runProjectImport(opts: ReconcileOptions): Promise<Reconcil
 			}
 
 			// Has agentuity.json but no access - offer to import
-			if (!interactive) {
+			if (!interactive && !opts.confirm) {
 				return {
 					status: 'error',
 					message:
@@ -635,10 +717,12 @@ export async function runProjectImport(opts: ReconcileOptions): Promise<Reconcil
 				};
 			}
 
-			return await importExistingProject(opts, projectConfig, userOrgs);
+			return await importExistingProject(opts, projectConfig, userOrgs, {
+				skipPrompt: opts.confirm,
+			});
 		} catch {
 			// Project doesn't exist - offer to import
-			if (!interactive) {
+			if (!interactive && !opts.confirm) {
 				return {
 					status: 'error',
 					message: 'Project not found. Run interactively to import it to your organization.',
@@ -646,14 +730,16 @@ export async function runProjectImport(opts: ReconcileOptions): Promise<Reconcil
 			}
 
 			const userOrgs = await listOrganizations(apiClient);
-			return await importExistingProject(opts, projectConfig, userOrgs);
+			return await importExistingProject(opts, projectConfig, userOrgs, {
+				skipPrompt: opts.confirm,
+			});
 		}
 	}
 
 	// No agentuity.json - validate structure and create new project
 	const isValid = await isValidProjectStructure(dir);
 
-	if (!isValid) {
+	if (!isValid && !opts.confirm) {
 		return {
 			status: 'error',
 			message:
@@ -670,7 +756,7 @@ export async function runProjectImport(opts: ReconcileOptions): Promise<Reconcil
 		};
 	}
 
-	if (!interactive) {
+	if (!interactive && !opts.confirm) {
 		return {
 			status: 'error',
 			message: 'Project import requires interactive mode.',

package/src/cmd/project/remote-import.ts

@@ -62,6 +62,8 @@ export interface RemoteImportOptions {
 	env?: string[];
 	org?: string;
 	region?: string;
+	/** If true, skip confirmation prompts (--confirm flag) */
+	confirm?: boolean;
 	apiClient: APIClient;
 	auth: AuthData;
 	config: Config;
@@ -744,7 +746,7 @@ export async function runRemoteImport(options: RemoteImportOptions): Promise<voi
 				optRegion,
 				org
 			);
-		} else if (isTTY()) {
+		} else if (isTTY() && !options.confirm) {
 			// Interactive mode: prompt for org/region/name
 			projectInfo = await createProjectInteractive(apiClient, config, logger, parsed.repo);
 		} else {
@@ -893,7 +895,7 @@ export async function runRemoteImport(options: RemoteImportOptions): Promise<voi
 		}
 
 		const resourceEnvVars: Record<string, string> = {};
-		const interactive = isTTY();
+		const interactive = isTTY() && !options.confirm;
 		const templateResources = template?.requirements?.resources ?? [];
 		const templateEnvVars = template?.requirements?.env ?? [];
 

package/src/config.ts

@@ -10,7 +10,7 @@ import {
 	APIClient as ServerAPIClient,
 } from '@agentuity/server';
 import { YAML } from 'bun';
-import JSON5 from 'json5';
+import { parseJSONC } from './utils/jsonc';
 import { z } from 'zod';
 import { clearProfileCache } from './cache';
 import { getCatalystUrl } from './catalyst';
@@ -141,6 +141,8 @@ function expandTilde(path: string): string {
 }
 
 let cachedConfig: Config | null | undefined;
+// Track the resolved config path so saveConfig writes back to the same file
+let cachedConfigPath: string | undefined;
 
 export async function loadConfig(
 	customPath?: string,
@@ -217,6 +219,7 @@ export async function loadConfig(
 		// This ensures --config flag is respected across all commands
 		if (!skipCache) {
 			cachedConfig = result.data;
+			cachedConfigPath = configPath;
 		}
 		return result.data;
 	} catch (error) {
@@ -227,6 +230,7 @@ export async function loadConfig(
 		// Note: For long-running processes, consider time-based cache expiry for transient failures.
 		if (!skipCache) {
 			cachedConfig = null;
+			cachedConfigPath = configPath;
 		}
 		return null;
 	}
@@ -261,8 +265,19 @@ function formatYAML(obj: unknown, indent = 0): string {
 		} else if (typeof value === 'string') {
 			if (value === '') {
 				lines.push(`${spaces}${key}: ""`);
-			} else if (value.includes(':') || value.includes('#') || value.includes(' ')) {
-				lines.push(`${spaces}${key}: "${value}"`);
+			} else if (
+				value.includes(':') ||
+				value.includes('#') ||
+				value.includes(' ') ||
+				value.includes('\\')
+			) {
+				// Use single quotes to avoid YAML escape-sequence processing.
+				// Double-quoted YAML strings interpret backslash sequences (\n, \t, etc.),
+				// which breaks Windows paths like C:\Users\... where \U would be invalid.
+				// Single-quoted strings treat backslashes literally.
+				// Escape any embedded single quotes by doubling them (YAML spec).
+				const escaped = value.replace(/'/g, "''");
+				lines.push(`${spaces}${key}: '${escaped}'`);
 			} else {
 				lines.push(`${spaces}${key}: ${value}`);
 			}
@@ -275,7 +290,10 @@ function formatYAML(obj: unknown, indent = 0): string {
 }
 
 export async function saveConfig(config: Config, customPath?: string): Promise<void> {
-	const configPath = customPath || (await getProfile());
+	// Use the path the config was originally loaded from (cachedConfigPath) so that
+	// saves go back to the correct profile even when --profile was used to load it.
+	// Falls back to getProfile() if no config has been loaded yet.
+	const configPath = customPath || cachedConfigPath || (await getProfile());
 	await ensureConfigDir();
 
 	const content = formatYAML(config);
@@ -595,7 +613,7 @@ export async function loadProjectConfig(
 		throw new ProjectConfigNotFoundException({ message: 'project config not found' });
 	}
 	const text = await file.text();
-	const parsedConfig = JSON5.parse(text);
+	const parsedConfig = parseJSONC(text);
 	const result = ProjectSchema.safeParse(parsedConfig);
 	if (!result.success) {
 		tui.error(`Invalid project config at ${configPath}:`);
@@ -700,7 +718,7 @@ export async function updateProjectConfig(
 	}
 
 	const text = await file.text();
-	const existing = JSON5.parse(text);
+	const existing = parseJSONC(text) as Record<string, unknown>;
 	const updated = { ...existing, ...updates };
 
 	const result = ProjectSchema.safeParse(updated);

package/src/schema-parser.ts

@@ -443,8 +443,14 @@ export function buildValidationInput(
 			const camelCaseName = opt.name.replace(/-([a-z])/g, (_, letter) => letter.toUpperCase());
 			let value = rawOptions[opt.name] ?? rawOptions[camelCaseName];
 
-			// Handle --yes alias for --confirm: if confirm is not set but yes is, use yes value
-			if (opt.name === 'confirm' && value === undefined && rawOptions.yes === true) {
+			// Handle --yes and --force aliases for --confirm: if confirm is not set but yes/force is, use that value
+			// Only treat --force as a --confirm alias if the schema does NOT declare a separate 'force' option
+			if (
+				opt.name === 'confirm' &&
+				value === undefined &&
+				(rawOptions.yes === true ||
+					(rawOptions.force === true && !parsed.some((o) => o.name === 'force')))
+			) {
 				value = true;
 			}
 

package/src/utils/jsonc.ts

@@ -0,0 +1,67 @@
+/**
+ * Parse JSON with Comments (JSONC).
+ *
+ * Strips single-line (`//`) and block (`/* *​/`) comments as well as trailing
+ * commas that appear before `}` or `]`, then delegates to the built-in
+ * `JSON.parse`.  This covers the comment syntax used by `tsconfig.json` and
+ * similar config files without pulling in a full JSON5 parser.
+ *
+ * String literals are respected — comments and trailing commas inside quoted
+ * strings are left untouched.
+ */
+export function parseJSONC(text: string): unknown {
+	let result = '';
+	let i = 0;
+	const len = text.length;
+
+	while (i < len) {
+		const ch = text[i];
+
+		// --- quoted string: copy verbatim, including any escape sequences ---
+		if (ch === '"') {
+			const start = i;
+			i++; // skip opening quote
+			while (i < len) {
+				if (text[i] === '\\') {
+					i += i + 1 < len ? 2 : 1; // skip escaped character (guard end-of-input)
+				} else if (text[i] === '"') {
+					i++; // skip closing quote
+					break;
+				} else {
+					i++;
+				}
+			}
+			result += text.slice(start, i);
+			continue;
+		}
+
+		// --- single-line comment: skip to end of line ---
+		if (ch === '/' && text[i + 1] === '/') {
+			i += 2;
+			while (i < len && text[i] !== '\n') {
+				i++;
+			}
+			continue;
+		}
+
+		// --- block comment: skip to closing *​/ ---
+		if (ch === '/' && text[i + 1] === '*') {
+			i += 2;
+			while (i < len && !(text[i] === '*' && text[i + 1] === '/')) {
+				i++;
+			}
+			if (i < len) {
+				i += 2; // skip closing */
+			}
+			continue;
+		}
+
+		result += ch;
+		i++;
+	}
+
+	// Strip trailing commas before } or ] (with optional whitespace between).
+	result = result.replace(/,(\s*[}\]])/g, '$1');
+
+	return JSON.parse(result);
+}

package/src/utils/route-migration.ts

@@ -697,7 +697,8 @@ export function performMigration(rootDir: string, routeFiles: string[]): Migrati
  * Show the migration notice and optionally perform migration.
  *
  * Called during `dev` and `build` after dependency upgrades.
- * Shows a banner the first time, then a shorter reminder on subsequent runs.
+ * Only prompts in interactive TTY sessions and only once — if the user
+ * dismisses the prompt, it won't be shown again.
  *
  * @returns true if migration was performed, false otherwise
  */
@@ -707,6 +708,12 @@ export async function promptRouteMigration(
 	options?: { interactive?: boolean }
 ): Promise<boolean> {
 	const interactive = options?.interactive ?? process.stdin.isTTY;
+
+	// Only show the interactive migration prompt in TTY sessions
+	if (!interactive) {
+		return false;
+	}
+
 	const eligibility = checkMigrationEligibility(rootDir);
 
 	if (!eligibility.available) {
@@ -715,48 +722,30 @@ export async function promptRouteMigration(
 
 	const { routeFiles, alreadyNotified } = eligibility;
 
-	// Non-interactive mode (CI, piped, AI agent): just log a notice
-	if (!interactive) {
-		if (!alreadyNotified) {
-			logger.info(
-				'[migration] This project uses file-based routing with %d route files in src/api/. ' +
-					'Agentuity is moving to explicit routing, which will become the default in the next major release. ' +
-					'Run `agentuity dev --migrate-routes` to migrate.',
-				routeFiles.length
-			);
-			writeMigrationState(rootDir, 'notified');
-		}
+	// Only prompt once — if the user has already been notified or dismissed, don't ask again
+	if (alreadyNotified) {
 		return false;
 	}
 
-	// First time: show full banner
-	if (!alreadyNotified) {
-		tui.newline();
-		tui.banner(
-			'✨ Migrate to Explicit Routing',
-			'Agentuity is moving to explicit routing, which will become the\n' +
-				'default in the next major release. File-based route discovery\n' +
-				'will be deprecated.\n' +
-				'\n' +
-				`Your project has ${routeFiles.length} route files in src/api/ that are\n` +
-				'auto-discovered at build time. Explicit routing gives you a single\n' +
-				'src/api/index.ts that imports and mounts all sub-routers — just\n' +
-				'like a standard Hono application.\n' +
-				'\n' +
-				`${tui.muted('Before:')} ${routeFiles.length} files auto-discovered from src/api/**/*.ts\n` +
-				`${tui.muted('After:')}  One src/api/index.ts that imports and mounts them\n` +
-				'\n' +
-				'Your existing route files are not modified. Your app.ts will be\n' +
-				'updated to import the router and pass it to createApp({ router }).',
-			{ centerTitle: false }
-		);
-	} else {
-		// Subsequent runs: shorter reminder
-		tui.newline();
-		tui.info(
-			`${tui.bold('Explicit routing migration available')} — run with ${tui.muted('--migrate-routes')} or choose below.`
-		);
-	}
+	tui.newline();
+	tui.banner(
+		'✨ Migrate to Explicit Routing',
+		'Agentuity is moving to explicit routing, which will become the\n' +
+			'default in the next major release. File-based route discovery\n' +
+			'will be deprecated.\n' +
+			'\n' +
+			`Your project has ${routeFiles.length} route files in src/api/ that are\n` +
+			'auto-discovered at build time. Explicit routing gives you a single\n' +
+			'src/api/index.ts that imports and mounts all sub-routers — just\n' +
+			'like a standard Hono application.\n' +
+			'\n' +
+			`${tui.muted('Before:')} ${routeFiles.length} files auto-discovered from src/api/**/*.ts\n` +
+			`${tui.muted('After:')}  One src/api/index.ts that imports and mounts them\n` +
+			'\n' +
+			'Your existing route files are not modified. Your app.ts will be\n' +
+			'updated to import the router and pass it to createApp({ router }).',
+		{ centerTitle: false }
+	);
 
 	tui.newline();
 

package/src/utils/zip.ts

@@ -1,3 +1,4 @@
+import { readFileSync, lstatSync } from 'node:fs';
 import { relative } from 'node:path';
 import { Glob } from 'bun';
 import AdmZip from 'adm-zip';
@@ -11,7 +12,7 @@ interface Options {
 export async function zipDir(dir: string, outdir: string, options?: Options) {
 	const zip = new AdmZip();
 	const files = await Array.fromAsync(
-		new Glob('**/*').scan({ cwd: dir, absolute: true, dot: true })
+		new Glob('**/*').scan({ cwd: dir, absolute: true, dot: true, followSymlinks: false })
 	);
 	const total = files.length;
 	let count = 0;
@@ -24,7 +25,21 @@ export async function zipDir(dir: string, outdir: string, options?: Options) {
 			}
 		}
 		if (!skip) {
-			zip.addLocalFile(file, undefined, rel);
+			try {
+				// Skip symlinks and directories — symlinks are workspace artefacts
+				// (e.g. bun's node_modules links) that cannot be resolved portably
+				// across machines and would cause EISDIR errors on extraction.
+				const stat = lstatSync(file);
+				if (!stat.isSymbolicLink() && !stat.isDirectory()) {
+					// Use addFile with explicit Unix permissions (0o644) instead of addLocalFile.
+					// On Windows, addLocalFile relies on OS file stats which may produce zip entries
+					// with incorrect Unix permission bits, causing EACCES errors when extracted on Linux.
+					const data = readFileSync(file);
+					zip.addFile(rel, data, '', 0o644);
+				}
+			} catch (err) {
+				throw new Error(`Failed to add file to zip: ${rel} (${file})`, { cause: err });
+			}
 		}
 		count++;
 		if (options?.progress) {