@gajae-code/coding-agent 0.11.1 → 0.11.2

package/src/lsp/client.ts

@@ -509,7 +509,7 @@ export async function getOrCreateClient(config: ServerConfig, cwd: string, initT
 
 		// Wrap with lspmux if available and supported
 		const { command, args, env } = isLspmuxSupported(baseCommand)
-			? await getLspmuxCommand(baseCommand, baseArgs)
+			? await getLspmuxCommand(baseCommand, baseArgs, cwd)
 			: { command: baseCommand, args: baseArgs };
 
 		const owner = spawnOwnedProcess([command, ...args], {

package/src/lsp/config.ts

@@ -8,6 +8,7 @@ import { type ClaudePluginRoot, getPreloadedPluginRoots } from "../discovery/hel
 import { BiomeClient } from "./clients/biome-client";
 import { SwiftLintClient } from "./clients/swiftlint-client";
 import DEFAULTS from "./defaults.json" with { type: "json" };
+import { isProjectControlledPath } from "./path-trust";
 import type { ServerConfig } from "./types";
 
 export interface LspConfig {
@@ -69,6 +70,40 @@ function normalizeExtensionToFileTypes(value: unknown): string[] | null {
 	return extensions.length > 0 ? extensions : null;
 }
 
+function sanitizeServerConfig(config: unknown, allowProcessOverrides: boolean): RawServerConfig | null {
+	if (!isRecord(config)) return null;
+
+	const sanitized: RawServerConfig = {};
+	if (allowProcessOverrides && typeof config.command === "string" && config.command.length > 0) {
+		sanitized.command = config.command;
+	}
+	if (allowProcessOverrides && Array.isArray(config.args)) {
+		sanitized.args = config.args.filter((entry): entry is string => typeof entry === "string");
+	}
+
+	const fileTypes = normalizeStringArray(config.fileTypes);
+	if (fileTypes) sanitized.fileTypes = fileTypes;
+	if (isRecord(config.extensionToLanguage)) sanitized.extensionToLanguage = config.extensionToLanguage;
+
+	const rootMarkers = normalizeStringArray(config.rootMarkers);
+	if (rootMarkers) sanitized.rootMarkers = rootMarkers;
+	if (allowProcessOverrides && isRecord(config.initOptions)) sanitized.initOptions = config.initOptions;
+	if (allowProcessOverrides && isRecord(config.initializationOptions)) {
+		sanitized.initializationOptions = config.initializationOptions;
+	}
+	if (allowProcessOverrides && isRecord(config.settings)) sanitized.settings = config.settings;
+	if (typeof config.disabled === "boolean") sanitized.disabled = config.disabled;
+	if (typeof config.warmupTimeoutMs === "number" && Number.isFinite(config.warmupTimeoutMs)) {
+		sanitized.warmupTimeoutMs = config.warmupTimeoutMs;
+	}
+	if (isRecord(config.capabilities)) sanitized.capabilities = config.capabilities;
+	const supersedes = normalizeStringArray(config.supersedes);
+	if (supersedes) sanitized.supersedes = supersedes;
+	if (typeof config.isLinter === "boolean") sanitized.isLinter = config.isLinter;
+
+	return sanitized;
+}
+
 function normalizeServerConfig(name: string, config: RawServerConfig): ServerConfig | null {
 	const command = typeof config.command === "string" && config.command.length > 0 ? config.command : null;
 	const fileTypes =
@@ -91,13 +126,17 @@ function normalizeServerConfig(name: string, config: RawServerConfig): ServerCon
 	const supersedes = normalizeStringArray(config.supersedes);
 
 	return {
-		...config,
 		command,
-		args,
+		...(args ? { args } : {}),
 		fileTypes,
 		rootMarkers,
 		...(initOptions ? { initOptions } : {}),
+		...(isRecord(config.settings) ? { settings: config.settings } : {}),
+		...(typeof config.disabled === "boolean" ? { disabled: config.disabled } : {}),
+		...(typeof config.warmupTimeoutMs === "number" ? { warmupTimeoutMs: config.warmupTimeoutMs } : {}),
+		...(isRecord(config.capabilities) ? { capabilities: config.capabilities } : {}),
 		...(supersedes ? { supersedes } : {}),
+		...(typeof config.isLinter === "boolean" ? { isLinter: config.isLinter } : {}),
 	};
 }
 
@@ -114,7 +153,8 @@ function readConfigFile(filePath: string): NormalizedConfig | null {
 function coerceServerConfigs(servers: Record<string, RawServerConfig>): Record<string, ServerConfig> {
 	const result: Record<string, ServerConfig> = {};
 	for (const [name, config] of Object.entries(servers)) {
-		const normalized = normalizeServerConfig(name, config);
+		const sanitized = sanitizeServerConfig(config, true);
+		const normalized = sanitized ? normalizeServerConfig(name, sanitized) : null;
 		if (normalized) {
 			result[name] = normalized;
 		}
@@ -125,11 +165,30 @@ function coerceServerConfigs(servers: Record<string, RawServerConfig>): Record<s
 function mergeServers(
 	base: Record<string, ServerConfig>,
 	overrides: Record<string, RawServerConfig>,
+	allowProcessOverrides: boolean,
 ): Record<string, ServerConfig> {
 	const merged: Record<string, ServerConfig> = { ...base };
 	for (const [name, config] of Object.entries(overrides)) {
+		if (
+			!allowProcessOverrides &&
+			isRecord(config) &&
+			("command" in config ||
+				"args" in config ||
+				"resolvedCommand" in config ||
+				"createClient" in config ||
+				"initOptions" in config ||
+				"initializationOptions" in config ||
+				"settings" in config)
+		) {
+			logger.warn("Ignoring project-controlled LSP process-affecting overrides.", { name });
+		}
+		const sanitized = sanitizeServerConfig(config, allowProcessOverrides);
+		if (!sanitized) {
+			logger.warn("Ignoring invalid LSP server config.", { name });
+			continue;
+		}
 		if (merged[name]) {
-			const candidate = { ...merged[name], ...config };
+			const candidate = { ...merged[name], ...sanitized };
 			const normalized = normalizeServerConfig(name, candidate);
 			if (normalized) {
 				merged[name] = normalized;
@@ -137,7 +196,7 @@ function mergeServers(
 				logger.warn("Ignoring invalid LSP overrides (keeping previous config).", { name });
 			}
 		} else {
-			const normalized = normalizeServerConfig(name, config);
+			const normalized = normalizeServerConfig(name, sanitized);
 			if (normalized) {
 				merged[name] = normalized;
 			}
@@ -276,17 +335,49 @@ export function resolveCommand(command: string, cwd: string): string | null {
 	return $which(command);
 }
 
+/** Resolve an LSP executable without consulting project-controlled bin directories. */
+function resolveTrustedLspCommand(command: string, cwd: string): string | null {
+	if (!path.isAbsolute(command) && (command.includes("/") || command.includes("\\"))) return null;
+	const discovered = path.isAbsolute(command) ? command : $which(command);
+	if (!discovered) return null;
+	if (isProjectControlledPath(discovered, cwd)) return null;
+	const canonical = canonicalExistingPath(discovered);
+	return canonical;
+}
+
 interface ConfigSource {
-	read(): NormalizedConfig | null;
+	allowProcessOverrides: boolean;
+	read(): LoadedConfigSource | null;
+}
+
+interface LoadedConfigSource {
+	config: NormalizedConfig;
+	projectControlled: boolean;
+}
+
+function canonicalExistingPath(filePath: string): string | null {
+	try {
+		return fs.realpathSync(filePath);
+	} catch {
+		return null;
+	}
 }
 
-function fileConfigSource(filePath: string): ConfigSource {
+function readCanonicalConfigFile(filePath: string, cwd: string): LoadedConfigSource | null {
+	const canonicalPath = canonicalExistingPath(filePath);
+	if (!canonicalPath) return null;
+	const config = readConfigFile(canonicalPath);
+	return config ? { config, projectControlled: isProjectControlledPath(canonicalPath, cwd) } : null;
+}
+
+function fileConfigSource(filePath: string, cwd: string, allowProcessOverrides: boolean): ConfigSource {
 	return {
-		read: () => readConfigFile(filePath),
+		allowProcessOverrides,
+		read: () => readCanonicalConfigFile(filePath, cwd),
 	};
 }
 
-function readMarketplaceLspConfig(root: ClaudePluginRoot): NormalizedConfig | null {
+function readMarketplaceLspConfig(root: ClaudePluginRoot, cwd: string): LoadedConfigSource | null {
 	const catalogPaths = [
 		path.resolve(root.path, "..", "..", "marketplace.json"),
 		path.resolve(root.path, "..", "..", ".claude-plugin", "marketplace.json"),
@@ -294,8 +385,11 @@ function readMarketplaceLspConfig(root: ClaudePluginRoot): NormalizedConfig | nu
 
 	for (const catalogPath of catalogPaths) {
 		try {
-			const catalog = JSON.parse(fs.readFileSync(catalogPath, "utf-8")) as unknown;
+			const canonicalCatalogPath = canonicalExistingPath(catalogPath);
+			if (!canonicalCatalogPath) continue;
+			const catalog = JSON.parse(fs.readFileSync(canonicalCatalogPath, "utf-8")) as unknown;
 			if (!isRecord(catalog) || !Array.isArray(catalog.plugins)) continue;
+			const catalogIsProjectControlled = isProjectControlledPath(canonicalCatalogPath, cwd);
 
 			for (const plugin of catalog.plugins) {
 				if (!isRecord(plugin) || plugin.name !== root.plugin) continue;
@@ -304,10 +398,27 @@ function readMarketplaceLspConfig(root: ClaudePluginRoot): NormalizedConfig | nu
 				if (typeof lspServers === "string") {
 					const configPath = path.resolve(root.path, lspServers);
 					if (!pathIsWithin(root.path, configPath)) return null;
-					return readConfigFile(configPath);
+					const canonicalRootPath = canonicalExistingPath(root.path);
+					const canonicalConfigPath = canonicalExistingPath(configPath);
+					if (
+						!canonicalRootPath ||
+						!canonicalConfigPath ||
+						!pathIsWithin(canonicalRootPath, canonicalConfigPath)
+					) {
+						return null;
+					}
+					const config = readConfigFile(canonicalConfigPath);
+					return config
+						? {
+								config,
+								projectControlled:
+									catalogIsProjectControlled || isProjectControlledPath(canonicalConfigPath, cwd),
+							}
+						: null;
 				}
 				if (isRecord(lspServers)) {
-					return normalizeConfig({ servers: lspServers });
+					const config = normalizeConfig({ servers: lspServers });
+					return config ? { config, projectControlled: catalogIsProjectControlled } : null;
 				}
 				return null;
 			}
@@ -317,12 +428,17 @@ function readMarketplaceLspConfig(root: ClaudePluginRoot): NormalizedConfig | nu
 	return null;
 }
 
-function marketplaceConfigSource(root: ClaudePluginRoot): ConfigSource {
+function marketplaceConfigSource(root: ClaudePluginRoot, cwd: string, allowProcessOverrides: boolean): ConfigSource {
 	return {
-		read: () => readMarketplaceLspConfig(root),
+		allowProcessOverrides,
+		read: () => readMarketplaceLspConfig(root, cwd),
 	};
 }
 
+function pluginCanOverrideProcess(root: ClaudePluginRoot, cwd: string): boolean {
+	return root.scope !== "project" && !isProjectControlledPath(root.path, cwd);
+}
+
 /**
  * Configuration sources in priority order.
  * Supports both visible and hidden variants at each config location.
@@ -333,14 +449,14 @@ function getConfigSources(cwd: string): ConfigSource[] {
 
 	// Project root files (highest priority)
 	for (const filename of filenames) {
-		sources.push(fileConfigSource(path.join(cwd, filename)));
+		sources.push(fileConfigSource(path.join(cwd, filename), cwd, false));
 	}
 
 	// Project config directories (.gjc/, .gemini/)
 	const projectDirs = getConfigDirPaths("", { user: false, project: true, cwd });
 	for (const dir of projectDirs) {
 		for (const filename of filenames) {
-			sources.push(fileConfigSource(path.join(dir, filename)));
+			sources.push(fileConfigSource(path.join(dir, filename), cwd, false));
 		}
 	}
 
@@ -348,22 +464,23 @@ function getConfigSources(cwd: string): ConfigSource[] {
 	const userDirs = getConfigDirPaths("", { user: true, project: false });
 	for (const dir of userDirs) {
 		for (const filename of filenames) {
-			sources.push(fileConfigSource(path.join(dir, filename)));
+			sources.push(fileConfigSource(path.join(dir, filename), cwd, true));
 		}
 	}
 
-	// Plugin LSP configs (from marketplace/--plugin-dir roots)
+	// Plugin LSP configs
 	const pluginRoots = getPreloadedPluginRoots();
 	for (const root of pluginRoots) {
+		const allowProcessOverrides = pluginCanOverrideProcess(root, cwd);
 		for (const filename of filenames) {
-			sources.push(fileConfigSource(path.join(root.path, filename)));
+			sources.push(fileConfigSource(path.join(root.path, filename), cwd, allowProcessOverrides));
 		}
-		sources.push(marketplaceConfigSource(root));
+		sources.push(marketplaceConfigSource(root, cwd, allowProcessOverrides));
 	}
 
 	// User home root files (lowest priority fallback)
 	for (const filename of filenames) {
-		sources.push(fileConfigSource(path.join(os.homedir(), filename)));
+		sources.push(fileConfigSource(path.join(os.homedir(), filename), cwd, true));
 	}
 
 	return sources;
@@ -408,12 +525,14 @@ export function loadConfig(cwd: string): LspConfig {
 
 	let idleTimeoutMs: number | undefined;
 	for (const source of configSources) {
-		const parsed = source.read();
-		if (!parsed) continue;
+		const loaded = source.read();
+		if (!loaded) continue;
+		const parsed = loaded.config;
+		const allowProcessOverrides = source.allowProcessOverrides && !loaded.projectControlled;
 		const hasServerOverrides = Object.keys(parsed.servers).length > 0;
 		if (hasServerOverrides) {
 			hasOverrides = true;
-			mergedServers = mergeServers(mergedServers, parsed.servers);
+			mergedServers = mergeServers(mergedServers, parsed.servers, allowProcessOverrides);
 		}
 		if (parsed.idleTimeoutMs !== undefined) {
 			idleTimeoutMs = parsed.idleTimeoutMs;
@@ -430,7 +549,7 @@ export function loadConfig(cwd: string): LspConfig {
 			if (!hasRootMarkers(cwd, config.rootMarkers)) continue;
 
 			// Check if the language server binary is available (local or $PATH)
-			const resolved = resolveCommand(config.command, cwd);
+			const resolved = resolveTrustedLspCommand(config.command, cwd);
 			if (!resolved) continue;
 
 			detected[name] = { ...config, resolvedCommand: resolved };
@@ -445,7 +564,7 @@ export function loadConfig(cwd: string): LspConfig {
 	for (const [name, config] of Object.entries(mergedWithRuntime)) {
 		if (config.disabled) continue;
 		if (!hasRootMarkers(cwd, config.rootMarkers)) continue;
-		const resolved = resolveCommand(config.command, cwd);
+		const resolved = resolveTrustedLspCommand(config.command, cwd);
 		if (!resolved) continue;
 		available[name] = { ...config, resolvedCommand: resolved };
 	}

package/src/lsp/index.ts

@@ -1213,7 +1213,7 @@ export class LspTool implements AgentTool<typeof lspSchema, LspToolDetails, Them
 		// Status action doesn't need a file
 		if (action === "status") {
 			const servers = Object.keys(config.servers);
-			const lspmuxState = await detectLspmux();
+			const lspmuxState = await detectLspmux(this.session.cwd);
 			const lspmuxStatus = lspmuxState.available
 				? lspmuxState.running
 					? "lspmux: active (multiplexing enabled)"

package/src/lsp/lspmux.ts

@@ -1,8 +1,10 @@
+import * as fs from "node:fs";
 import * as os from "node:os";
 import * as path from "node:path";
 import { $flag, $which, logger } from "@gajae-code/utils";
 import { TOML } from "bun";
 import { spawnOwnedProcess } from "../runtime/process-lifecycle";
+import { isProjectControlledPath } from "./path-trust";
 
 /**
  * lspmux integration for LSP server multiplexing.
@@ -81,6 +83,7 @@ function getConfigPath(): string {
 
 let cachedState: LspmuxState | null = null;
 let cacheTimestamp = 0;
+let cacheCwd: string | null = null;
 
 /**
  * Parse lspmux config.toml file.
@@ -110,7 +113,7 @@ async function checkServerRunning(binaryPath: string): Promise<boolean> {
 		drainStream(proc.stdout);
 		drainStream(proc.stderr);
 
-		let timer: ReturnType<typeof setTimeout> | undefined;
+		let timer: NodeJS.Timeout | undefined;
 		const timeout = new Promise<null>(resolve => {
 			timer = setTimeout(() => resolve(null), LIVENESS_TIMEOUT_MS);
 		});
@@ -147,28 +150,42 @@ function drainStream(stream: ReadableStream<Uint8Array> | null | undefined): voi
 	})();
 }
 
+function resolveTrustedLspmuxBinary(cwd: string): string | null {
+	const discoveredPath = $which("lspmux");
+	if (!discoveredPath) return null;
+	if (isProjectControlledPath(discoveredPath, cwd)) return null;
+
+	try {
+		return fs.realpathSync(discoveredPath);
+	} catch {
+		return null;
+	}
+}
+
 /**
  * Detect lspmux availability and state.
  * Results are cached for STATE_CACHE_TTL_MS.
  *
- * Set PI_DISABLE_LSPMUX=1 to disable.
+ * Set GJC_DISABLE_LSPMUX=1 or PI_DISABLE_LSPMUX=1 to disable.
  */
-export async function detectLspmux(): Promise<LspmuxState> {
+export async function detectLspmux(cwd = process.cwd()): Promise<LspmuxState> {
 	const now = Date.now();
-	if (cachedState && now - cacheTimestamp < STATE_CACHE_TTL_MS) {
+	if ($flag("GJC_DISABLE_LSPMUX") || $flag("PI_DISABLE_LSPMUX")) {
+		cachedState = { available: false, running: false, binaryPath: null, config: null };
+		cacheTimestamp = now;
+		cacheCwd = cwd;
 		return cachedState;
 	}
 
-	if ($flag("PI_DISABLE_LSPMUX")) {
-		cachedState = { available: false, running: false, binaryPath: null, config: null };
-		cacheTimestamp = now;
+	if (cachedState && cacheCwd === cwd && now - cacheTimestamp < STATE_CACHE_TTL_MS) {
 		return cachedState;
 	}
 
-	const binaryPath = $which("lspmux");
+	const binaryPath = resolveTrustedLspmuxBinary(cwd);
 	if (!binaryPath) {
 		cachedState = { available: false, running: false, binaryPath: null, config: null };
 		cacheTimestamp = now;
+		cacheCwd = cwd;
 		return cachedState;
 	}
 
@@ -176,6 +193,7 @@ export async function detectLspmux(): Promise<LspmuxState> {
 
 	cachedState = { available: true, running, binaryPath, config };
 	cacheTimestamp = now;
+	cacheCwd = cwd;
 
 	if (running) {
 		logger.debug("lspmux detected and running", { binaryPath });
@@ -184,6 +202,13 @@ export async function detectLspmux(): Promise<LspmuxState> {
 	return cachedState;
 }
 
+/** Reset cached lspmux detection state for focused tests. */
+export function resetLspmuxStateForTesting(): void {
+	cachedState = null;
+	cacheTimestamp = 0;
+	cacheCwd = null;
+}
+
 // =============================================================================
 // Command Wrapping
 // =============================================================================
@@ -251,7 +276,11 @@ export function wrapWithLspmux(
  * @param args - Original command arguments
  * @returns Command and args to use (possibly wrapped with lspmux)
  */
-export async function getLspmuxCommand(command: string, args?: string[]): Promise<LspmuxWrappedCommand> {
-	const state = await detectLspmux();
+export async function getLspmuxCommand(
+	command: string,
+	args?: string[],
+	cwd = process.cwd(),
+): Promise<LspmuxWrappedCommand> {
+	const state = await detectLspmux(cwd);
 	return wrapWithLspmux(command, args, state);
 }

package/src/lsp/path-trust.ts

@@ -0,0 +1,81 @@
+import * as fs from "node:fs";
+import * as os from "node:os";
+import * as path from "node:path";
+import { CONFIG_DIR_NAME, pathIsWithin, relativePathEscapesRoot } from "@gajae-code/utils";
+
+function normalizePathForComparison(candidate: string): string {
+	const resolved = path.resolve(candidate);
+	return process.platform === "win32" ? resolved.toLowerCase() : resolved;
+}
+
+function pathIsLexicallyWithin(root: string, candidate: string): boolean {
+	const relative = path.relative(normalizePathForComparison(root), normalizePathForComparison(candidate));
+	return !relativePathEscapesRoot(relative);
+}
+
+function canonicalPath(candidate: string): string {
+	try {
+		return fs.realpathSync(candidate);
+	} catch {
+		return path.resolve(candidate);
+	}
+}
+
+function canonicalParentPath(candidate: string): string {
+	const resolved = path.resolve(candidate);
+	return path.join(canonicalPath(path.dirname(resolved)), path.basename(resolved));
+}
+
+function isDirectory(candidate: string): boolean {
+	try {
+		return fs.statSync(candidate).isDirectory();
+	} catch {
+		return false;
+	}
+}
+
+function pathMatchesStop(candidate: string, stopPaths: ReadonlySet<string>): boolean {
+	return (
+		stopPaths.has(normalizePathForComparison(candidate)) ||
+		stopPaths.has(normalizePathForComparison(canonicalPath(candidate)))
+	);
+}
+
+function findProjectTrustRoot(start: string, stopPaths: ReadonlySet<string>): string | undefined {
+	const fallback = path.resolve(start);
+	let nearestConfigRoot: string | undefined;
+	let current = fallback;
+	for (;;) {
+		if (pathMatchesStop(current, stopPaths)) {
+			return current === fallback ? undefined : (nearestConfigRoot ?? fallback);
+		}
+		if (fs.existsSync(path.join(current, ".git"))) return current;
+		if (nearestConfigRoot === undefined && isDirectory(path.join(current, CONFIG_DIR_NAME))) {
+			nearestConfigRoot = current;
+		}
+		const parent = path.dirname(current);
+		if (parent === current) return nearestConfigRoot ?? fallback;
+		current = parent;
+	}
+}
+
+export function isProjectControlledPath(candidate: string, cwd: string): boolean {
+	const home = os.homedir();
+	const stopPaths = new Set([path.resolve(home), canonicalPath(home)].map(normalizePathForComparison));
+	const lexicalTrustRoot = findProjectTrustRoot(cwd, stopPaths);
+	if (lexicalTrustRoot !== undefined && pathIsLexicallyWithin(lexicalTrustRoot, candidate)) return true;
+
+	const canonicalTrustRoots = new Set<string>();
+	if (lexicalTrustRoot !== undefined) canonicalTrustRoots.add(canonicalPath(lexicalTrustRoot));
+	const canonicalTrustRoot = findProjectTrustRoot(canonicalPath(cwd), stopPaths);
+	if (canonicalTrustRoot !== undefined) canonicalTrustRoots.add(canonicalTrustRoot);
+	for (const trustRoot of canonicalTrustRoots) {
+		if (
+			pathIsLexicallyWithin(trustRoot, canonicalParentPath(candidate)) ||
+			pathIsWithin(trustRoot, canonicalPath(candidate))
+		) {
+			return true;
+		}
+	}
+	return false;
+}

package/src/main.ts

@@ -57,6 +57,7 @@ import type { AgentSession } from "./session/agent-session";
 import {
 	type ResumeSessionIdentity,
 	resolveResumableSession,
+	type SessionDirectoryMigrationPolicy,
 	type SessionInfo,
 	SessionManager,
 	type StrictSessionOpenResult,
@@ -510,6 +511,7 @@ type SelectResumeSession = (sessions: SessionInfo[]) => Promise<SessionSelection
 type OpenExistingSessionStrict = (
 	identity: ResumeSessionIdentity,
 	sessionDir?: string,
+	migrationPolicy?: SessionDirectoryMigrationPolicy,
 ) => Promise<StrictSessionOpenResult>;
 
 export const BARE_RESUME_CONFLICT_ERROR =
@@ -694,6 +696,7 @@ export async function createSessionManager(
 	cwd: string,
 	activeSettings: Settings = settings,
 ): Promise<SessionManager | undefined> {
+	const migrationPolicy = activeSettings.get("session.directoryMigration") === "disabled" ? "disabled" : "copy-retain";
 	if (parsed.resume === true) {
 		return undefined;
 	}
@@ -703,13 +706,13 @@ export async function createSessionManager(
 		}
 		const forkSource = parsed.fork;
 		if (forkSource.includes("/") || forkSource.includes("\\") || forkSource.endsWith(".jsonl")) {
-			return await SessionManager.forkFrom(forkSource, cwd, parsed.sessionDir);
+			return await SessionManager.forkFrom(forkSource, cwd, parsed.sessionDir, undefined, migrationPolicy);
 		}
 		const match = await resolveResumableSession(forkSource, cwd, parsed.sessionDir);
 		if (!match) {
 			throw new Error(`Session "${forkSource}" not found.`);
 		}
-		return await SessionManager.forkFrom(match.session.path, cwd, parsed.sessionDir);
+		return await SessionManager.forkFrom(match.session.path, cwd, parsed.sessionDir, undefined, migrationPolicy);
 	}
 
 	if (parsed.noSession) {
@@ -718,7 +721,7 @@ export async function createSessionManager(
 	if (typeof parsed.resume === "string") {
 		const sessionArg = parsed.resume;
 		if (sessionArg.includes("/") || sessionArg.includes("\\") || sessionArg.endsWith(".jsonl")) {
-			return await SessionManager.open(sessionArg, parsed.sessionDir);
+			return await SessionManager.open(sessionArg, parsed.sessionDir, undefined, migrationPolicy);
 		}
 		const match = await resolveResumableSession(sessionArg, cwd, parsed.sessionDir);
 		if (!match) {
@@ -732,13 +735,19 @@ export async function createSessionManager(
 				if (!shouldFork) {
 					throw new Error(`Session "${sessionArg}" is in another project (${match.session.cwd}).`);
 				}
-				return await SessionManager.forkFrom(match.session.path, cwd, parsed.sessionDir);
+				return await SessionManager.forkFrom(
+					match.session.path,
+					cwd,
+					parsed.sessionDir,
+					undefined,
+					migrationPolicy,
+				);
 			}
 		}
-		return await SessionManager.open(match.session.path, parsed.sessionDir);
+		return await SessionManager.open(match.session.path, parsed.sessionDir, undefined, migrationPolicy);
 	}
 	if (parsed.continue) {
-		return await SessionManager.continueRecent(cwd, parsed.sessionDir);
+		return await SessionManager.continueRecent(cwd, parsed.sessionDir, undefined, migrationPolicy);
 	}
 	// --resume without value is handled separately (needs picker UI)
 	// If --session-dir provided without --continue/--resume, create new session there
@@ -761,7 +770,7 @@ export async function createSessionManager(
 	// buildSessionOptions restores the session's model/thinking instead of
 	// overriding them with CLI defaults.
 	if (activeSettings.get("autoResume")) {
-		const manager = await SessionManager.continueRecent(cwd, parsed.sessionDir);
+		const manager = await SessionManager.continueRecent(cwd, parsed.sessionDir, undefined, migrationPolicy);
 		if (manager.getEntries().length > 0) {
 			parsed.continue = true;
 		}
@@ -1014,6 +1023,7 @@ export interface RunRootCommandDependencies {
 	selectResumeSession?: SelectResumeSession;
 	openExistingSessionStrict?: OpenExistingSessionStrict;
 	initializeSettings?: typeof Settings.init;
+	loadSettingsForScope?: typeof Settings.loadForScope;
 }
 
 export async function runRootCommand(
@@ -1054,15 +1064,25 @@ export async function runRootCommand(
 			process.stdout.write(`${chalk.dim("No sessions found")}\n`);
 			return;
 		}
-		const selection = await (deps.selectResumeSession ?? selectSession)(sessions);
+		const selection = deps.selectResumeSession
+			? await deps.selectResumeSession(sessions)
+			: await selectSession(sessions, parsedArgs.sessionDir);
 		if (selection.kind === "cancelled") {
 			return;
 		}
+		const resumeMigrationPolicy =
+			(await (deps.loadSettingsForScope ?? Settings.loadForScope)({ cwd: resumeCwd })).get(
+				"session.directoryMigration",
+			) === "disabled"
+				? "disabled"
+				: "copy-retain";
 		let opened: StrictSessionOpenResult;
 		try {
 			opened = await (deps.openExistingSessionStrict ?? SessionManager.openExistingStrict)(
 				selection.identity,
 				parsedArgs.sessionDir,
+				undefined,
+				resumeMigrationPolicy,
 			);
 		} catch {
 			process.stderr.write(`${BARE_RESUME_OPEN_ERROR}\n`);

package/src/memories/index.ts

@@ -249,6 +249,7 @@ async function runPhase1(options: {
 
 		const claims = claimStage1Jobs(db, {
 			nowSec,
+			cwd: session.sessionManager.getCwd(),
 			threadScanLimit: config.threadScanLimit,
 			maxRolloutsPerStartup: config.maxRolloutsPerStartup,
 			maxRolloutAgeDays: config.maxRolloutAgeDays,

package/src/memories/storage.ts

@@ -137,6 +137,7 @@ export function claimStage1Jobs(
 	db: Database,
 	params: {
 		nowSec: number;
+		cwd: string;
 		threadScanLimit: number;
 		maxRolloutsPerStartup: number;
 		maxRolloutAgeDays: number;
@@ -149,6 +150,7 @@ export function claimStage1Jobs(
 ): Stage1Claim[] {
 	const {
 		nowSec,
+		cwd,
 		threadScanLimit,
 		maxRolloutsPerStartup,
 		maxRolloutAgeDays,
@@ -168,8 +170,10 @@ export function claimStage1Jobs(
 	let runningCount = runningCountRow?.count ?? 0;
 	if (runningCount >= runningConcurrencyCap) return [];
 	const candidateRows = db
-		.prepare("SELECT id, updated_at, rollout_path, cwd, source_kind FROM threads ORDER BY updated_at DESC LIMIT ?")
-		.all(threadScanLimit) as Array<{
+		.prepare(
+			"SELECT id, updated_at, rollout_path, cwd, source_kind FROM threads WHERE cwd = ? ORDER BY updated_at DESC LIMIT ?",
+		)
+		.all(cwd, threadScanLimit) as Array<{
 		id: string;
 		updated_at: number;
 		rollout_path: string;