Improve project-local pi config (#6309)

* feat(coding-agent): improve config resource overrides

* fix(coding-agent): simplify config resource overrides

packages/coding-agent/docs/packages.md

@@ -216,11 +216,11 @@ Filter what a package loads using the object form in settings:
 
 ## Enable and Disable Resources
 
-Use `pi config` to enable or disable extensions, skills, prompt templates, and themes from installed packages and local directories. Works for both global (`~/.pi/agent`) and project (`.pi/`) scopes.
+Use `pi config` to enable or disable extensions, skills, prompt templates, and themes from installed packages and local directories. `pi config` starts in global settings (`~/.pi/agent/settings.json`); press Tab to switch between global and project-local modes. Use `pi config -l` to start in project overrides (`.pi/settings.json`) with inherited global resources dimmed.
 
 ## Scope and Deduplication
 
-Packages can appear in both global and project settings. If the same package appears in both, the project entry wins. Identity is determined by:
+Packages can appear in both global and project settings. If the same package appears in both, the project entry wins unless the project entry has `autoload: false`, in which case it is applied as a delta over the global entry. Identity is determined by:
 
 - npm: package name
 - git: repository URL without ref

packages/coding-agent/src/cli/args.ts

@@ -231,8 +231,8 @@ ${chalk.bold("Commands:")}
   ${APP_NAME} uninstall <source> [-l]   Alias for remove
   ${APP_NAME} update [source|self|pi]   Update pi (use --all for pi and extensions)
   ${APP_NAME} list                      List installed extensions from settings
-  ${APP_NAME} config                    Open TUI to enable/disable package resources
-  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list
+  ${APP_NAME} config [-l]               Open TUI to enable/disable package resources (Tab switches scope)
+  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list/config
 
 ${chalk.bold("Options:")}
   --provider <name>              Provider name (default: google)

packages/coding-agent/src/cli/config-selector.ts

@@ -3,16 +3,17 @@
  */
 
 import { ProcessTerminal, TUI } from "@earendil-works/pi-tui";
-import type { ResolvedPaths } from "../core/package-manager.ts";
 import type { SettingsManager } from "../core/settings-manager.ts";
-import { ConfigSelectorComponent } from "../modes/interactive/components/config-selector.ts";
+import { ConfigSelectorComponent, type ScopedResolvedPaths } from "../modes/interactive/components/config-selector.ts";
 import { initTheme, stopThemeWatcher } from "../modes/interactive/theme/theme.ts";
 
 export interface ConfigSelectorOptions {
-	resolvedPaths: ResolvedPaths;
+	resolvedPaths: ScopedResolvedPaths;
 	settingsManager: SettingsManager;
 	cwd: string;
 	agentDir: string;
+	writeScope: "global" | "project";
+	projectModeAvailable: boolean;
 }
 
 /** Show TUI config selector and return when closed */
@@ -44,6 +45,8 @@ export async function selectConfig(options: ConfigSelectorOptions): Promise<void
 			},
 			() => ui.requestRender(),
 			ui.terminal.rows,
+			options.writeScope,
+			options.projectModeAvailable,
 		);
 
 		ui.addChild(selector);

packages/coding-agent/src/core/package-manager.ts

@@ -188,6 +188,7 @@ function resourcePrecedenceRank(m: PathMetadata): number {
 }
 
 interface PackageFilter {
+	autoload?: boolean;
 	extensions?: string[];
 	skills?: string[];
 	prompts?: string[];
@@ -772,6 +773,25 @@ function applyPatterns(allPaths: string[], patterns: string[], baseDir: string):
 	return new Set(result);
 }
 
+function applyAutoloadDisabledPatterns(allPaths: string[], patterns: string[], baseDir: string): Map<string, boolean> {
+	const result = new Map<string, boolean>();
+	for (const pattern of patterns) {
+		const target = pattern.slice(
+			pattern.startsWith("+") || pattern.startsWith("-") || pattern.startsWith("!") ? 1 : 0,
+		);
+		const enabled = !pattern.startsWith("-") && !pattern.startsWith("!");
+		const exact = pattern.startsWith("+") || pattern.startsWith("-");
+		for (const filePath of allPaths) {
+			if (
+				exact ? matchesAnyExactPattern(filePath, [target], baseDir) : matchesAnyPattern(filePath, [target], baseDir)
+			) {
+				result.set(filePath, enabled);
+			}
+		}
+	}
+	return result;
+}
+
 export class DefaultPackageManager implements PackageManager {
 	private cwd: string;
 	private agentDir: string;
@@ -1225,38 +1245,39 @@ export class DefaultPackageManager implements PackageManager {
 		for (const { pkg, scope } of sources) {
 			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
 			const filter = typeof pkg === "object" ? pkg : undefined;
-			const parsed = this.parseSource(sourceStr);
+			const deltaBase = this.findAutoloadDeltaBase(pkg, scope, sources);
+			const resolvedSource = deltaBase?.source ?? sourceStr;
+			const resolvedScope = deltaBase?.scope ?? scope;
+			const parsed = this.parseSource(resolvedSource);
 			const metadata: PathMetadata = { source: sourceStr, scope, origin: "package" };
 
 			if (parsed.type === "local") {
-				const baseDir = this.getBaseDirForScope(scope);
+				const baseDir = this.getBaseDirForScope(resolvedScope);
 				this.resolveLocalExtensionSource(parsed, accumulator, filter, metadata, baseDir);
 				continue;
 			}
 
 			const installMissing = async (): Promise<boolean> => {
-				if (isOfflineModeEnabled()) {
-					return false;
-				}
+				if (isOfflineModeEnabled()) return false;
 				if (!onMissing) {
-					await this.installParsedSource(parsed, scope);
+					await this.installParsedSource(parsed, resolvedScope);
 					return true;
 				}
-				const action = await onMissing(sourceStr);
+				const action = await onMissing(resolvedSource);
 				if (action === "skip") return false;
-				if (action === "error") throw new Error(`Missing source: ${sourceStr}`);
-				await this.installParsedSource(parsed, scope);
+				if (action === "error") throw new Error(`Missing source: ${resolvedSource}`);
+				await this.installParsedSource(parsed, resolvedScope);
 				return true;
 			};
 
 			if (parsed.type === "npm") {
-				let installedPath = this.getNpmInstallPath(parsed, scope);
+				let installedPath = this.getNpmInstallPath(parsed, resolvedScope);
 				const needsInstall =
 					!existsSync(installedPath) || !(await this.installedNpmMatchesConfiguredVersion(parsed, installedPath));
 				if (needsInstall) {
 					const installed = await installMissing();
 					if (!installed) continue;
-					installedPath = this.getNpmInstallPath(parsed, scope);
+					installedPath = this.getNpmInstallPath(parsed, resolvedScope);
 				}
 				metadata.baseDir = installedPath;
 				this.collectPackageResources(installedPath, accumulator, filter, metadata);
@@ -1264,12 +1285,12 @@ export class DefaultPackageManager implements PackageManager {
 			}
 
 			if (parsed.type === "git") {
-				const installedPath = this.getGitInstallPath(parsed, scope);
+				const installedPath = this.getGitInstallPath(parsed, resolvedScope);
 				if (!existsSync(installedPath)) {
 					const installed = await installMissing();
 					if (!installed) continue;
-				} else if (scope === "temporary" && !parsed.pinned && !isOfflineModeEnabled()) {
-					await this.refreshTemporaryGitSource(parsed, sourceStr);
+				} else if (resolvedScope === "temporary" && !parsed.pinned && !isOfflineModeEnabled()) {
+					await this.refreshTemporaryGitSource(parsed, resolvedSource);
 				}
 				metadata.baseDir = installedPath;
 				this.collectPackageResources(installedPath, accumulator, filter, metadata);
@@ -1277,6 +1298,21 @@ export class DefaultPackageManager implements PackageManager {
 		}
 	}
 
+	private findAutoloadDeltaBase(
+		pkg: PackageSource,
+		scope: SourceScope,
+		sources: Array<{ pkg: PackageSource; scope: SourceScope }>,
+	): { source: string; scope: SourceScope } | undefined {
+		if (scope !== "project" || typeof pkg !== "object" || pkg.autoload !== false) return undefined;
+		const identity = this.getPackageIdentity(pkg.source, scope);
+		const userEntry = sources.find(
+			(entry) =>
+				entry.scope === "user" &&
+				this.getPackageIdentity(this.getPackageSourceString(entry.pkg), "user") === identity,
+		);
+		return userEntry ? { source: this.getPackageSourceString(userEntry.pkg), scope: "user" } : undefined;
+	}
+
 	private resolveLocalExtensionSource(
 		source: LocalSource,
 		accumulator: ResourceAccumulator,
@@ -1655,29 +1691,30 @@ export class DefaultPackageManager implements PackageManager {
 
 	/**
 	 * Dedupe packages: if same package identity appears in both global and project,
-	 * keep only the project one (project wins).
+	 * keep only the project one (project wins). A project entry with autoload=false
+	 * is a delta over the global entry, so both are kept (delta first).
 	 */
 	private dedupePackages(
 		packages: Array<{ pkg: PackageSource; scope: SourceScope }>,
 	): Array<{ pkg: PackageSource; scope: SourceScope }> {
-		const seen = new Map<string, { pkg: PackageSource; scope: SourceScope }>();
-
+		const result: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
+		const seen = new Map<string, number>();
 		for (const entry of packages) {
-			const sourceStr = typeof entry.pkg === "string" ? entry.pkg : entry.pkg.source;
-			const identity = this.getPackageIdentity(sourceStr, entry.scope);
-
-			const existing = seen.get(identity);
-			if (!existing) {
-				seen.set(identity, entry);
-			} else if (entry.scope === "project" && existing.scope === "user") {
-				// Project wins over user
-				seen.set(identity, entry);
+			const identity = this.getPackageIdentity(this.getPackageSourceString(entry.pkg), entry.scope);
+			const index = seen.get(identity);
+			if (index === undefined) {
+				seen.set(identity, result.length);
+				result.push(entry);
+				continue;
+			}
+			const existing = result[index];
+			if (existing?.scope === "project" && entry.scope === "user") {
+				if (typeof existing.pkg === "object" && existing.pkg.autoload === false) result.push(entry);
+			} else if (entry.scope === "project") {
+				result[index] = entry;
 			}
-			// If existing is project and new is global, keep existing (project)
-			// If both are same scope, keep first one
 		}
-
-		return Array.from(seen.values());
+		return result;
 	}
 
 	private parseNpmSpec(spec: string): { name: string; version?: string } {
@@ -2047,9 +2084,11 @@ export class DefaultPackageManager implements PackageManager {
 	): boolean {
 		if (filter) {
 			for (const resourceType of RESOURCE_TYPES) {
-				const patterns = filter[resourceType as keyof PackageFilter];
+				const patterns = filter[resourceType];
 				const target = this.getTargetMap(accumulator, resourceType);
-				if (patterns !== undefined) {
+				if (filter.autoload === false) {
+					this.applyPackageDeltaFilter(packageRoot, patterns ?? [], resourceType, target, metadata);
+				} else if (patterns !== undefined) {
 					this.applyPackageFilter(packageRoot, patterns, resourceType, target, metadata);
 				} else {
 					this.collectDefaultResources(packageRoot, resourceType, target, metadata);
@@ -2136,6 +2175,24 @@ export class DefaultPackageManager implements PackageManager {
 		}
 	}
 
+	private applyPackageDeltaFilter(
+		packageRoot: string,
+		userPatterns: string[],
+		resourceType: ResourceType,
+		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
+		metadata: PathMetadata,
+	): void {
+		if (userPatterns.length === 0) {
+			return;
+		}
+
+		const { allFiles } = this.collectManifestFiles(packageRoot, resourceType);
+		const enabledByUser = applyAutoloadDisabledPatterns(allFiles, userPatterns, packageRoot);
+		for (const [filePath, enabled] of enabledByUser) {
+			this.addResource(target, filePath, metadata, enabled);
+		}
+	}
+
 	/**
 	 * Collect all files from a package for a resource type, applying manifest patterns.
 	 * Returns { allFiles, enabledByManifest } where enabledByManifest is the set of files

packages/coding-agent/src/core/settings-manager.ts

@@ -66,11 +66,13 @@ export type TransportSetting = Transport;
  * Package source for npm/git packages.
  * - String form: load all resources from the package
  * - Object form: filter which resources to load
+ * - autoload=false: start empty and only apply explicit resource patterns
  */
 export type PackageSource =
 	| string
 	| {
 			source: string;
+			autoload?: boolean;
 			extensions?: string[];
 			skills?: string[];
 			prompts?: string[];

packages/coding-agent/src/modes/interactive/components/config-selector.ts

@@ -18,11 +18,18 @@ import {
 import { CONFIG_DIR_NAME } from "../../../config.ts";
 import type { PathMetadata, ResolvedPaths, ResolvedResource } from "../../../core/package-manager.ts";
 import type { PackageSource, SettingsManager } from "../../../core/settings-manager.ts";
+import { canonicalizePath, isLocalPath, resolvePath } from "../../../utils/paths.ts";
 import { theme } from "../theme/theme.ts";
 import { DynamicBorder } from "./dynamic-border.ts";
-import { rawKeyHint } from "./keybinding-hints.ts";
+import { keyHint, rawKeyHint } from "./keybinding-hints.ts";
 
 type ResourceType = "extensions" | "skills" | "prompts" | "themes";
+type ConfigWriteScope = "global" | "project";
+type SettingsScope = "user" | "project";
+type ProjectOverrideState = "inherit" | "load" | "unload";
+export type ScopedResolvedPaths = Record<ConfigWriteScope, ResolvedPaths>;
+
+const RESOURCE_TYPES = ["extensions", "skills", "prompts", "themes"] as const satisfies readonly ResourceType[];
 
 const RESOURCE_TYPE_LABELS: Record<ResourceType, string> = {
 	extensions: "Extensions",
@@ -178,25 +185,42 @@ type FlatEntry =
 	| { type: "item"; item: ResourceItem };
 
 class ConfigSelectorHeader implements Component {
+	private writeScope: ConfigWriteScope;
+	private projectModeAvailable: boolean;
+
+	constructor(writeScope: ConfigWriteScope, projectModeAvailable: boolean) {
+		this.writeScope = writeScope;
+		this.projectModeAvailable = projectModeAvailable;
+	}
+
+	setWriteScope(writeScope: ConfigWriteScope): void {
+		this.writeScope = writeScope;
+	}
+
 	invalidate(): void {}
 
 	render(width: number): string[] {
-		const title = theme.bold("Resource Configuration");
+		const title = theme.bold(this.writeScope === "project" ? "Project Local Resources" : "Global Resources");
 		const sep = theme.fg("muted", " · ");
-		const hint = rawKeyHint("space", "toggle") + sep + rawKeyHint("esc", "close");
-		const hintWidth = visibleWidth(hint);
-		const titleWidth = visibleWidth(title);
-		const spacing = Math.max(1, width - titleWidth - hintWidth);
+		const switchHint = this.projectModeAvailable ? keyHint("tui.input.tab", "switch mode") + sep : "";
+		const actionHint =
+			this.writeScope === "project" ? rawKeyHint("space", "cycle inherit/+/-") : rawKeyHint("space", "toggle");
+		const hint = switchHint + actionHint + sep + rawKeyHint("esc", "close");
+		const spacing = Math.max(1, width - visibleWidth(title) - visibleWidth(hint));
+		const scopeHint =
+			this.writeScope === "project"
+				? theme.fg("muted", `${CONFIG_DIR_NAME}/settings.json · inherited global resources are dimmed`)
+				: theme.fg("muted", `~/${CONFIG_DIR_NAME}/agent/settings.json`);
 
 		return [
 			truncateToWidth(`${title}${" ".repeat(spacing)}${hint}`, width, ""),
-			theme.fg("muted", "Type to filter resources"),
+			truncateToWidth(scopeHint, width, ""),
 		];
 	}
 }
 
 class ResourceList implements Component, Focusable {
-	private groups: ResourceGroup[];
+	private groupsByScope: Record<ConfigWriteScope, ResourceGroup[]>;
 	private flatItems: FlatEntry[] = [];
 	private filteredItems: FlatEntry[] = [];
 	private selectedIndex = 0;
@@ -205,10 +229,13 @@ class ResourceList implements Component, Focusable {
 	private settingsManager: SettingsManager;
 	private cwd: string;
 	private agentDir: string;
+	private writeScope: ConfigWriteScope;
+	private inheritedEnabledByKey: Map<string, boolean>;
 
 	public onCancel?: () => void;
 	public onExit?: () => void;
 	public onToggle?: (item: ResourceItem, newEnabled: boolean) => void;
+	public onSwitchMode?: () => void;
 
 	private _focused = false;
 	get focused(): boolean {
@@ -220,16 +247,19 @@ class ResourceList implements Component, Focusable {
 	}
 
 	constructor(
-		groups: ResourceGroup[],
+		groupsByScope: Record<ConfigWriteScope, ResourceGroup[]>,
 		settingsManager: SettingsManager,
 		cwd: string,
 		agentDir: string,
 		terminalHeight?: number,
+		writeScope: ConfigWriteScope = "global",
 	) {
-		this.groups = groups;
+		this.groupsByScope = groupsByScope;
 		this.settingsManager = settingsManager;
 		this.cwd = cwd;
 		this.agentDir = agentDir;
+		this.writeScope = writeScope;
+		this.inheritedEnabledByKey = this.buildInheritedEnabledMap(groupsByScope.global);
 		this.searchInput = new Input();
 		// 8 lines of chrome: top spacer + top border + spacer + header (2 lines) + spacer + bottom spacer + bottom border
 		const chrome = 8;
@@ -238,6 +268,28 @@ class ResourceList implements Component, Focusable {
 		this.filteredItems = [...this.flatItems];
 	}
 
+	setWriteScope(writeScope: ConfigWriteScope): void {
+		this.writeScope = writeScope;
+		this.buildFlatList();
+		this.filterItems(this.searchInput.getValue());
+	}
+
+	private get groups(): ResourceGroup[] {
+		return this.groupsByScope[this.writeScope];
+	}
+
+	private buildInheritedEnabledMap(groups: ResourceGroup[]): Map<string, boolean> {
+		const result = new Map<string, boolean>();
+		for (const group of groups) {
+			for (const subgroup of group.subgroups) {
+				for (const item of subgroup.items) {
+					result.set(this.getResourceItemKey(item), item.enabled);
+				}
+			}
+		}
+		return result;
+	}
+
 	private buildFlatList(): void {
 		this.flatItems = [];
 		for (const group of this.groups) {
@@ -362,19 +414,29 @@ class ResourceList implements Component, Focusable {
 
 			if (entry.type === "group") {
 				// Main group header (no cursor)
-				const groupLine = theme.fg("accent", theme.bold(entry.group.label));
+				const inherited = this.writeScope === "project" && entry.group.scope === "user";
+				const label = theme.bold(`${entry.group.label}${inherited ? " · inherited global" : ""}`);
+				const groupLine = theme.fg(inherited ? "dim" : "accent", label);
 				lines.push(truncateToWidth(`  ${groupLine}`, width, ""));
 			} else if (entry.type === "subgroup") {
 				// Subgroup header (indented, no cursor)
-				const subgroupLine = theme.fg("muted", entry.subgroup.label);
+				const color = this.writeScope === "project" && entry.group.scope === "user" ? "dim" : "muted";
+				const subgroupLine = theme.fg(color, entry.subgroup.label);
 				lines.push(truncateToWidth(`    ${subgroupLine}`, width, ""));
 			} else {
 				// Resource item (cursor only on items)
 				const item = entry.item;
 				const cursor = isSelected ? "> " : "  ";
-				const checkbox = item.enabled ? theme.fg("success", "[x]") : theme.fg("dim", "[ ]");
-				const name = isSelected ? theme.bold(item.displayName) : item.displayName;
-				lines.push(truncateToWidth(`${cursor}    ${checkbox} ${name}`, width, "..."));
+				const dimmed = this.isDimmedItem(item);
+				const nameText = isSelected && !dimmed ? theme.bold(item.displayName) : item.displayName;
+				const name = dimmed ? theme.fg("dim", nameText) : nameText;
+				lines.push(
+					truncateToWidth(
+						`${cursor}    ${this.renderCheckbox(item)} ${name}${this.getItemSuffix(item)}`,
+						width,
+						"...",
+					),
+				);
 			}
 		}
 
@@ -430,13 +492,18 @@ class ResourceList implements Component, Focusable {
 			this.onExit?.();
 			return;
 		}
+		if (kb.matches(data, "tui.input.tab")) {
+			this.onSwitchMode?.();
+			return;
+		}
 		if (data === " " || kb.matches(data, "tui.select.confirm")) {
 			const entry = this.filteredItems[this.selectedIndex];
-			if (entry?.type === "item") {
-				const newEnabled = !entry.item.enabled;
-				this.toggleResource(entry.item, newEnabled);
-				this.updateItem(entry.item, newEnabled);
-				this.onToggle?.(entry.item, newEnabled);
+			if (entry?.type === "item" && (this.writeScope === "project" || this.getItemScope(entry.item) === "user")) {
+				const newEnabled = this.toggleResource(entry.item);
+				if (newEnabled !== undefined) {
+					this.updateItem(entry.item, newEnabled);
+					this.onToggle?.(entry.item, newEnabled);
+				}
 			}
 			return;
 		}
@@ -446,12 +513,20 @@ class ResourceList implements Component, Focusable {
 		this.filterItems(this.searchInput.getValue());
 	}
 
-	private toggleResource(item: ResourceItem, enabled: boolean): void {
+	private toggleResource(item: ResourceItem): boolean | undefined {
+		if (this.writeScope === "project") {
+			const state = this.getNextOverrideState(item);
+			if (!this.setProjectResourceOverride(item, state)) return undefined;
+			return state === "inherit" ? this.getInheritedEnabled(item) : state === "load";
+		}
+
+		const enabled = !item.enabled;
 		if (item.metadata.origin === "top-level") {
 			this.toggleTopLevelResource(item, enabled);
 		} else {
 			this.togglePackageResource(item, enabled);
 		}
+		return enabled;
 	}
 
 	private toggleTopLevelResource(item: ResourceItem, enabled: boolean): void {
@@ -561,6 +636,217 @@ class ResourceList implements Component, Focusable {
 		}
 	}
 
+	private renderCheckbox(item: ResourceItem): string {
+		if (this.writeScope === "project") {
+			const state = this.getProjectOverrideState(item);
+			if (state === "load") return theme.fg("success", "[+]");
+			if (state === "unload") return theme.fg("warning", "[-]");
+			return theme.fg("dim", item.enabled ? "[x]" : "[ ]");
+		}
+		return item.enabled ? theme.fg("success", "[x]") : theme.fg("dim", "[ ]");
+	}
+
+	private getItemSuffix(item: ResourceItem): string {
+		if (this.writeScope !== "project") return "";
+		const state = this.getProjectOverrideState(item);
+		if (state === "load") return theme.fg("muted", "  project load");
+		if (state === "unload") return theme.fg("muted", "  project unload");
+		return this.isInheritedGlobalItem(item) ? theme.fg("dim", "  inherited global") : "";
+	}
+
+	private isDimmedItem(item: ResourceItem): boolean {
+		return (
+			this.writeScope === "project" &&
+			this.isInheritedGlobalItem(item) &&
+			this.getProjectOverrideState(item) === "inherit"
+		);
+	}
+
+	private setProjectResourceOverride(item: ResourceItem, state: ProjectOverrideState): boolean {
+		return item.metadata.origin === "top-level"
+			? this.setProjectTopLevelOverride(item, state)
+			: this.setProjectPackageOverride(item, state);
+	}
+
+	private setProjectTopLevelOverride(item: ResourceItem, state: ProjectOverrideState): boolean {
+		const current = (this.settingsManager.getProjectSettings()[item.resourceType] ?? []) as string[];
+		const pattern = this.isInheritedGlobalItem(item) ? item.path : this.getResourcePatternForScope(item, "project");
+		const patterns = this.getTopLevelOverridePatterns(item, "project");
+		const updated = current.filter((entry) => {
+			const target = this.getPatternEntryTarget(entry);
+			if ((entry.startsWith("!") || entry.startsWith("+") || entry.startsWith("-")) && patterns.has(target))
+				return false;
+			return !(state === "inherit" && this.isInheritedGlobalItem(item) && target === pattern);
+		});
+		if (state !== "inherit") {
+			if (this.isInheritedGlobalItem(item) && !updated.includes(pattern)) updated.push(pattern);
+			updated.push(`${state === "load" ? "+" : "-"}${pattern}`);
+		}
+		this.setProjectTopLevelPaths(item.resourceType, updated);
+		return true;
+	}
+
+	private setProjectTopLevelPaths(key: ResourceType, paths: string[]): void {
+		if (key === "extensions") this.settingsManager.setProjectExtensionPaths(paths);
+		else if (key === "skills") this.settingsManager.setProjectSkillPaths(paths);
+		else if (key === "prompts") this.settingsManager.setProjectPromptTemplatePaths(paths);
+		else this.settingsManager.setProjectThemePaths(paths);
+	}
+
+	private setProjectPackageOverride(item: ResourceItem, state: ProjectOverrideState): boolean {
+		const packages = [...(this.settingsManager.getProjectSettings().packages ?? [])] as PackageSource[];
+		let pkgIndex = packages.findIndex((pkg) =>
+			this.packageSourceStringMatches(
+				item.metadata.source,
+				this.getItemScope(item),
+				typeof pkg === "string" ? pkg : pkg.source,
+				"project",
+			),
+		);
+		if (pkgIndex === -1) {
+			if (state === "inherit") return false;
+			packages.push(this.createPackageOverrideSource(item));
+			pkgIndex = packages.length - 1;
+		}
+		let pkg = packages[pkgIndex];
+		if (pkg === undefined) return false;
+		if (typeof pkg === "string") {
+			pkg = { source: pkg };
+			packages[pkgIndex] = pkg;
+		}
+		const pattern = this.getPackageResourcePattern(item);
+		const updated = ((pkg[item.resourceType] ?? []) as string[]).filter(
+			(entry) => this.getPatternEntryTarget(entry) !== pattern,
+		);
+		if (state !== "inherit") updated.push(`${state === "load" ? "+" : "-"}${pattern}`);
+		(pkg as Record<string, unknown>)[item.resourceType] = updated.length > 0 ? updated : undefined;
+		if (!RESOURCE_TYPES.some((key) => (pkg as Record<string, unknown>)[key] !== undefined)) {
+			if (pkg.autoload === false) packages.splice(pkgIndex, 1);
+			else packages[pkgIndex] = pkg.source;
+		}
+		this.settingsManager.setProjectPackages(packages);
+		return true;
+	}
+
+	private getNextOverrideState(item: ResourceItem): ProjectOverrideState {
+		const state = this.getProjectOverrideState(item);
+		const inheritedEnabled = this.getInheritedEnabled(item);
+		if (state === "inherit") return inheritedEnabled ? "unload" : "load";
+		if (state === "unload") return inheritedEnabled ? "load" : "inherit";
+		return inheritedEnabled ? "inherit" : "unload";
+	}
+
+	private getProjectOverrideState(item: ResourceItem): ProjectOverrideState {
+		if (this.writeScope !== "project") return "inherit";
+		if (item.metadata.origin === "top-level") {
+			return this.getOverrideStateFromEntries(
+				(this.settingsManager.getProjectSettings()[item.resourceType] ?? []) as string[],
+				this.getTopLevelOverridePatterns(item, "project"),
+				false,
+			);
+		}
+		const pkg = this.findMatchingPackageSource(item, "project");
+		if (typeof pkg !== "object") return "inherit";
+		const entries = pkg[item.resourceType];
+		if (entries === undefined) return "inherit";
+		return this.getOverrideStateFromEntries(
+			entries,
+			new Set([this.getPackageResourcePattern(item)]),
+			pkg.autoload !== false,
+		);
+	}
+
+	private getOverrideStateFromEntries(
+		entries: string[],
+		patterns: Set<string>,
+		emptyArrayIsUnload: boolean,
+	): ProjectOverrideState {
+		if (entries.length === 0 && emptyArrayIsUnload) return "unload";
+		let state: ProjectOverrideState = "inherit";
+		for (const entry of entries) {
+			if (!patterns.has(this.getPatternEntryTarget(entry))) continue;
+			if (entry.startsWith("!") || entry.startsWith("-")) state = "unload";
+			else state = "load";
+		}
+		return state;
+	}
+
+	private getInheritedEnabled(item: ResourceItem): boolean {
+		return (
+			this.inheritedEnabledByKey.get(this.getResourceItemKey(item)) ??
+			(this.getItemScope(item) === "user" ? item.enabled : true)
+		);
+	}
+
+	private isInheritedGlobalItem(item: ResourceItem): boolean {
+		return this.getItemScope(item) === "user" || this.inheritedEnabledByKey.has(this.getResourceItemKey(item));
+	}
+
+	private getTopLevelOverridePatterns(item: ResourceItem, scope: SettingsScope): Set<string> {
+		const baseDir = this.getTopLevelBaseDir(scope);
+		const patterns = new Set<string>([
+			this.getResourcePatternForScope(item, scope),
+			item.path,
+			relative(baseDir, item.path),
+		]);
+		if (item.metadata.baseDir) patterns.add(relative(item.metadata.baseDir, item.path));
+		return patterns;
+	}
+
+	private getResourcePatternForScope(item: ResourceItem, scope: SettingsScope): string {
+		const sourceScope = this.getItemScope(item);
+		if (scope !== sourceScope) return item.path;
+		const baseDir = item.metadata.baseDir ?? this.getTopLevelBaseDir(sourceScope);
+		return relative(baseDir, item.path);
+	}
+
+	private createPackageOverrideSource(item: ResourceItem): PackageSource {
+		const source = item.metadata.source;
+		if (!isLocalPath(source)) return { source, autoload: false };
+		const sourcePath = resolvePath(source, this.getTopLevelBaseDir(this.getItemScope(item)), { trim: true });
+		return { source: relative(this.getTopLevelBaseDir("project"), sourcePath) || ".", autoload: false };
+	}
+
+	private packageSourceStringMatches(
+		leftSource: string,
+		leftScope: SettingsScope,
+		rightSource: string,
+		rightScope: SettingsScope,
+	): boolean {
+		if (leftSource === rightSource) return true;
+		if (!isLocalPath(leftSource) || !isLocalPath(rightSource)) return false;
+		const left = resolvePath(leftSource, this.getTopLevelBaseDir(leftScope), { trim: true });
+		const right = resolvePath(rightSource, this.getTopLevelBaseDir(rightScope), { trim: true });
+		return left === right;
+	}
+
+	private findMatchingPackageSource(item: ResourceItem, targetScope: SettingsScope): PackageSource | undefined {
+		const settings =
+			targetScope === "project"
+				? this.settingsManager.getProjectSettings()
+				: this.settingsManager.getGlobalSettings();
+		return (settings.packages ?? []).find((pkg) =>
+			this.packageSourceStringMatches(
+				item.metadata.source,
+				this.getItemScope(item),
+				typeof pkg === "string" ? pkg : pkg.source,
+				targetScope,
+			),
+		);
+	}
+
+	private getPatternEntryTarget(entry: string): string {
+		return entry.startsWith("!") || entry.startsWith("+") || entry.startsWith("-") ? entry.slice(1) : entry;
+	}
+
+	private getResourceItemKey(item: ResourceItem): string {
+		return `${item.resourceType}:${canonicalizePath(item.path)}`;
+	}
+
+	private getItemScope(item: ResourceItem): SettingsScope {
+		return item.metadata.scope === "project" ? "project" : "user";
+	}
+
 	private getTopLevelBaseDir(scope: "user" | "project"): string {
 		return scope === "project" ? join(this.cwd, CONFIG_DIR_NAME) : this.agentDir;
 	}
@@ -578,7 +864,9 @@ class ResourceList implements Component, Focusable {
 }
 
 export class ConfigSelectorComponent extends Container implements Focusable {
+	private header: ConfigSelectorHeader;
 	private resourceList: ResourceList;
+	private writeScope: ConfigWriteScope;
 
 	private _focused = false;
 	get focused(): boolean {
@@ -590,7 +878,7 @@ export class ConfigSelectorComponent extends Container implements Focusable {
 	}
 
 	constructor(
-		resolvedPaths: ResolvedPaths,
+		resolvedPaths: ScopedResolvedPaths,
 		settingsManager: SettingsManager,
 		cwd: string,
 		agentDir: string,
@@ -598,23 +886,43 @@ export class ConfigSelectorComponent extends Container implements Focusable {
 		onExit: () => void,
 		requestRender: () => void,
 		terminalHeight?: number,
+		writeScope: ConfigWriteScope = "global",
+		projectModeAvailable = true,
 	) {
 		super();
 
-		const groups = buildGroups(resolvedPaths, agentDir);
+		this.writeScope = writeScope;
+		const groupsByScope = {
+			global: buildGroups(resolvedPaths.global, agentDir),
+			project: buildGroups(resolvedPaths.project, agentDir),
+		};
 
 		// Add header
 		this.addChild(new Spacer(1));
 		this.addChild(new DynamicBorder());
 		this.addChild(new Spacer(1));
-		this.addChild(new ConfigSelectorHeader());
+		this.header = new ConfigSelectorHeader(this.writeScope, projectModeAvailable);
+		this.addChild(this.header);
 		this.addChild(new Spacer(1));
 
 		// Resource list
-		this.resourceList = new ResourceList(groups, settingsManager, cwd, agentDir, terminalHeight);
+		this.resourceList = new ResourceList(
+			groupsByScope,
+			settingsManager,
+			cwd,
+			agentDir,
+			terminalHeight,
+			this.writeScope,
+		);
 		this.resourceList.onCancel = onClose;
 		this.resourceList.onExit = onExit;
 		this.resourceList.onToggle = () => requestRender();
+		if (projectModeAvailable) {
+			this.resourceList.onSwitchMode = () => {
+				this.switchWriteScope();
+				requestRender();
+			};
+		}
 		this.addChild(this.resourceList);
 
 		// Bottom border
@@ -622,6 +930,12 @@ export class ConfigSelectorComponent extends Container implements Focusable {
 		this.addChild(new DynamicBorder());
 	}
 
+	private switchWriteScope(): void {
+		this.writeScope = this.writeScope === "global" ? "project" : "global";
+		this.header.setWriteScope(this.writeScope);
+		this.resourceList.setWriteScope(this.writeScope);
+	}
+
 	getResourceList(): ResourceList {
 		return this.resourceList;
 	}

packages/coding-agent/src/package-manager-cli.ts

@@ -87,6 +87,23 @@ function getPackageCommandUsage(command: PackageCommand): string {
 	}
 }
 
+const CONFIG_COMMAND_USAGE = `${APP_NAME} config [-l] [--approve|--no-approve]`;
+
+function printConfigCommandHelp(): void {
+	console.log(`${chalk.bold("Usage:")}
+  ${CONFIG_COMMAND_USAGE}
+
+Open the resource configuration TUI to enable or disable package resources.
+Without -l, starts in global settings (~/${CONFIG_DIR_NAME}/agent/settings.json).
+Press Tab in the TUI to switch between global and project-local modes.
+
+Options:
+  -l, --local       Edit project overrides (${CONFIG_DIR_NAME}/settings.json)
+  -a, --approve     Trust project-local files for this command with -l
+  -na, --no-approve Ignore project-local files for this command with -l
+`);
+}
+
 function printPackageCommandHelp(command: PackageCommand): void {
 	switch (command) {
 		case "install":
@@ -466,18 +483,6 @@ function prepareWindowsNpmSelfUpdate(): void {
 	quarantineWindowsNativeDependencies(packageDir);
 }
 
-function parseProjectTrustOverride(args: readonly string[]): boolean | undefined {
-	let trustOverride: boolean | undefined;
-	for (const arg of args) {
-		if (arg === "--approve" || arg === "-a") {
-			trustOverride = true;
-		} else if (arg === "--no-approve" || arg === "-na") {
-			trustOverride = false;
-		}
-	}
-	return trustOverride;
-}
-
 export interface PackageCommandRuntimeOptions {
 	extensionFactories?: ExtensionFactory[];
 }
@@ -549,28 +554,70 @@ export async function handleConfigCommand(
 	args: string[],
 	runtimeOptions: PackageCommandRuntimeOptions = {},
 ): Promise<boolean> {
-	if (args[0] !== "config") {
+	const [command, ...rest] = args;
+	if (command !== "config") {
 		return false;
 	}
 
+	if (rest.includes("-h") || rest.includes("--help")) {
+		printConfigCommandHelp();
+		return true;
+	}
+
+	let local = false;
+	let projectTrustOverride: boolean | undefined;
+	for (const arg of rest) {
+		if (arg === "-l" || arg === "--local") {
+			local = true;
+		} else if (arg === "-a" || arg === "--approve") {
+			projectTrustOverride = true;
+		} else if (arg === "-na" || arg === "--no-approve") {
+			projectTrustOverride = false;
+		} else if (arg.startsWith("-")) {
+			console.error(chalk.red(`Unknown option ${arg} for "config".`));
+			console.error(chalk.dim(`Use "${APP_NAME} --help" or "${CONFIG_COMMAND_USAGE}".`));
+			process.exitCode = 1;
+			return true;
+		} else {
+			console.error(chalk.red(`Unexpected argument ${arg}.`));
+			console.error(chalk.dim(`Usage: ${CONFIG_COMMAND_USAGE}`));
+			process.exitCode = 1;
+			return true;
+		}
+	}
+
 	const cwd = process.cwd();
 	const agentDir = getAgentDir();
 	const { settingsManager, projectTrustWarnings } = await createCommandSettingsManager({
 		cwd,
 		agentDir,
-		projectTrustOverride: parseProjectTrustOverride(args),
+		projectTrustOverride,
 		extensionFactories: runtimeOptions.extensionFactories,
 	});
 	reportProjectTrustWarnings(projectTrustWarnings);
+	if (local && !settingsManager.isProjectTrusted()) {
+		console.error(chalk.red("Project is not trusted. Use --approve to modify local resource config."));
+		process.exitCode = 1;
+		return true;
+	}
 	reportSettingsErrors(settingsManager, "config command");
-	const packageManager = new DefaultPackageManager({ cwd, agentDir, settingsManager });
-	const resolvedPaths = await packageManager.resolve();
+	const globalSettingsManager = SettingsManager.create(cwd, agentDir, { projectTrusted: false });
+	const globalResolvedPaths = await new DefaultPackageManager({
+		cwd,
+		agentDir,
+		settingsManager: globalSettingsManager,
+	}).resolve();
+	const projectResolvedPaths = settingsManager.isProjectTrusted()
+		? await new DefaultPackageManager({ cwd, agentDir, settingsManager }).resolve()
+		: globalResolvedPaths;
 
 	await selectConfig({
-		resolvedPaths,
+		resolvedPaths: { global: globalResolvedPaths, project: projectResolvedPaths },
 		settingsManager,
 		cwd,
 		agentDir,
+		writeScope: local ? "project" : "global",
+		projectModeAvailable: settingsManager.isProjectTrusted(),
 	});
 
 	process.exit(0);

packages/coding-agent/test/package-command-paths.test.ts

@@ -3,8 +3,11 @@ import { tmpdir } from "node:os";
 import { delimiter, join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import { ENV_AGENT_DIR, PACKAGE_NAME, VERSION } from "../src/config.ts";
+import type { ResolvedPaths } from "../src/core/package-manager.ts";
+import { InMemorySettingsStorage, SettingsManager } from "../src/core/settings-manager.ts";
 import { ProjectTrustStore } from "../src/core/trust-manager.ts";
 import { main } from "../src/main.ts";
+import { ConfigSelectorComponent } from "../src/modes/interactive/components/config-selector.ts";
 import { handlePackageCommand } from "../src/package-manager-cli.ts";
 
 describe("package commands", () => {
@@ -28,6 +31,24 @@ describe("package commands", () => {
 		expect(await handlePackageCommand(args)).toBe(true);
 	}
 
+	function extensionPaths(
+		packageRoot: string,
+		source: string,
+		scope: "user" | "project",
+		names: string[],
+	): ResolvedPaths {
+		return {
+			extensions: names.map((name) => ({
+				path: join(packageRoot, "extensions", name),
+				enabled: true,
+				metadata: { source, scope, origin: "package", baseDir: packageRoot },
+			})),
+			skills: [],
+			prompts: [],
+			themes: [],
+		};
+	}
+
 	beforeEach(() => {
 		tempDir = join(tmpdir(), `pi-package-commands-${Date.now()}-${Math.random().toString(36).slice(2)}`);
 		agentDir = join(tempDir, "agent");
@@ -350,6 +371,37 @@ describe("package commands", () => {
 		}
 	});
 
+	it("cycles project package overrides in config local mode", async () => {
+		const storage = new InMemorySettingsStorage();
+		storage.withLock("global", () => JSON.stringify({ packages: ["npm:pi-tools"] }));
+		const settingsManager = SettingsManager.fromStorage(storage, { projectTrusted: true });
+		const resolvedPaths = extensionPaths(join(tempDir, "pkg"), "npm:pi-tools", "user", ["bar.ts"]);
+		const selector = new ConfigSelectorComponent(
+			{ global: resolvedPaths, project: resolvedPaths },
+			settingsManager,
+			projectDir,
+			agentDir,
+			() => {},
+			() => {},
+			() => {},
+			24,
+			"project",
+		);
+
+		selector.getResourceList().handleInput(" ");
+		expect(settingsManager.getProjectSettings().packages).toEqual([
+			{ source: "npm:pi-tools", autoload: false, extensions: ["-extensions/bar.ts"] },
+		]);
+
+		selector.getResourceList().handleInput(" ");
+		expect(settingsManager.getProjectSettings().packages).toEqual([
+			{ source: "npm:pi-tools", autoload: false, extensions: ["+extensions/bar.ts"] },
+		]);
+
+		selector.getResourceList().handleInput(" ");
+		expect(settingsManager.getProjectSettings().packages).toEqual([]);
+	});
+
 	it("shows a friendly error for unknown install options", async () => {
 		const errorSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 

packages/coding-agent/test/package-manager.test.ts

@@ -1674,6 +1674,49 @@ Content`,
 			expect(result.extensions.some((r) => isEnabled(r, "one.ts"))).toBe(true);
 			expect(result.extensions.some((r) => isDisabled(r, "two.ts"))).toBe(true);
 		});
+
+		it("should resolve autoload-disabled project package entries as deltas over global packages", async () => {
+			const pkgDir = join(agentDir, "npm", "node_modules", "pi-tools");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "package.json"), JSON.stringify({ name: "pi-tools", version: "1.0.0" }));
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			settingsManager.setPackages(["npm:pi-tools"]);
+			settingsManager.setProjectPackages([
+				{ source: "npm:pi-tools", autoload: false, extensions: ["-extensions/foo.ts"] },
+			]);
+			const runCommandSpy = vi
+				.spyOn(packageManager as unknown as PackageManagerInternals, "runCommand")
+				.mockRejectedValue(new Error("unexpected install"));
+
+			const result = await packageManager.resolve();
+			const states = Object.fromEntries(
+				result.extensions.map((resource) => [
+					resource.path,
+					{ enabled: resource.enabled, scope: resource.metadata.scope },
+				]),
+			);
+			expect(runCommandSpy).not.toHaveBeenCalled();
+			expect(states[join(pkgDir, "extensions", "foo.ts")]).toEqual({ enabled: false, scope: "project" });
+			expect(states[join(pkgDir, "extensions", "bar.ts")]).toEqual({ enabled: true, scope: "user" });
+		});
+
+		it("should resolve autoload-disabled package entries as positive-only without a global package", async () => {
+			const pkgDir = join(tempDir, "positive-only-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "skills", "foo"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "skills", "foo", "SKILL.md"), "# Foo\n");
+			settingsManager.setProjectPackages([
+				{ source: relative(join(tempDir, ".pi"), pkgDir), autoload: false, extensions: ["+extensions/foo.ts"] },
+			]);
+
+			const result = await packageManager.resolve();
+
+			expect(result.extensions.map((resource) => resource.path)).toEqual([join(pkgDir, "extensions", "foo.ts")]);
+			expect(result.skills).toEqual([]);
+		});
 	});
 
 	describe("force-include patterns", () => {