feat(coding-agent): prioritize project resources over global

packages/coding-agent/CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## [Unreleased]
 
+### Breaking Changes
+
+- Resource precedence for extensions, skills, prompts, themes, and slash-command name collisions is now project-first (`cwd/.pi`) before user-global (`~/.pi/agent`). If you relied on global resources overriding project resources with the same names, rename or reorder your resources.
+- Extension registration conflicts no longer unload the entire later extension. All extensions stay loaded, and conflicting command/tool/flag names are resolved by first registration in load order.
+
 ## [0.54.2] - 2026-02-23
 
 ### Fixed

packages/coding-agent/src/core/extensions/loader.ts

@@ -173,7 +173,7 @@ function createExtensionAPI(
 			options: { description?: string; type: "boolean" | "string"; default?: boolean | string },
 		): void {
 			extension.flags.set(name, { name, extensionPath: extension.path, ...options });
-			if (options.default !== undefined) {
+			if (options.default !== undefined && !runtime.flagValues.has(name)) {
 				runtime.flagValues.set(name, options.default);
 			}
 		},
@@ -486,14 +486,14 @@ export async function discoverAndLoadExtensions(
 		}
 	};
 
-	// 1. Global extensions: agentDir/extensions/
-	const globalExtDir = path.join(agentDir, "extensions");
-	addPaths(discoverExtensionsInDir(globalExtDir));
-
-	// 2. Project-local extensions: cwd/.pi/extensions/
+	// 1. Project-local extensions: cwd/.pi/extensions/
 	const localExtDir = path.join(cwd, ".pi", "extensions");
 	addPaths(discoverExtensionsInDir(localExtDir));
 
+	// 2. Global extensions: agentDir/extensions/
+	const globalExtDir = path.join(agentDir, "extensions");
+	addPaths(discoverExtensionsInDir(globalExtDir));
+
 	// 3. Explicitly configured paths
 	for (const p of configuredPaths) {
 		const resolved = resolvePath(p, cwd);

packages/coding-agent/src/core/extensions/runner.ts

@@ -301,15 +301,17 @@ export class ExtensionRunner {
 		return this.extensions.map((e) => e.path);
 	}
 
-	/** Get all registered tools from all extensions. */
+	/** Get all registered tools from all extensions (first registration per name wins). */
 	getAllRegisteredTools(): RegisteredTool[] {
-		const tools: RegisteredTool[] = [];
+		const toolsByName = new Map<string, RegisteredTool>();
 		for (const ext of this.extensions) {
 			for (const tool of ext.tools.values()) {
-				tools.push(tool);
+				if (!toolsByName.has(tool.definition.name)) {
+					toolsByName.set(tool.definition.name, tool);
+				}
 			}
 		}
-		return tools;
+		return Array.from(toolsByName.values());
 	}
 
 	/** Get a tool definition by name. Returns undefined if not found. */
@@ -327,7 +329,9 @@ export class ExtensionRunner {
 		const allFlags = new Map<string, ExtensionFlag>();
 		for (const ext of this.extensions) {
 			for (const [name, flag] of ext.flags) {
-				allFlags.set(name, flag);
+				if (!allFlags.has(name)) {
+					allFlags.set(name, flag);
+				}
 			}
 		}
 		return allFlags;
@@ -425,6 +429,7 @@ export class ExtensionRunner {
 		this.commandDiagnostics = [];
 
 		const commands: RegisteredCommand[] = [];
+		const commandOwners = new Map<string, string>();
 		for (const ext of this.extensions) {
 			for (const command of ext.commands.values()) {
 				if (reserved?.has(command.name)) {
@@ -436,6 +441,17 @@ export class ExtensionRunner {
 					continue;
 				}
 
+				const existingOwner = commandOwners.get(command.name);
+				if (existingOwner) {
+					const message = `Extension command '${command.name}' from ${ext.path} conflicts with ${existingOwner}. Skipping.`;
+					this.commandDiagnostics.push({ type: "warning", message, path: ext.path });
+					if (!this.hasUI()) {
+						console.warn(message);
+					}
+					continue;
+				}
+
+				commandOwners.set(command.name, ext.path);
 				commands.push(command);
 			}
 		}

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

@@ -722,14 +722,14 @@ export class DefaultPackageManager implements PackageManager {
 		const globalSettings = this.settingsManager.getGlobalSettings();
 		const projectSettings = this.settingsManager.getProjectSettings();
 
-		// Collect all packages with scope
+		// Collect all packages with scope (project first so cwd resources win collisions)
 		const allPackages: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
-		for (const pkg of globalSettings.packages ?? []) {
-			allPackages.push({ pkg, scope: "user" });
-		}
 		for (const pkg of projectSettings.packages ?? []) {
 			allPackages.push({ pkg, scope: "project" });
 		}
+		for (const pkg of globalSettings.packages ?? []) {
+			allPackages.push({ pkg, scope: "user" });
+		}
 
 		// Dedupe: project scope wins over global for same package identity
 		const packageSources = this.dedupePackages(allPackages);
@@ -742,17 +742,6 @@ export class DefaultPackageManager implements PackageManager {
 			const target = this.getTargetMap(accumulator, resourceType);
 			const globalEntries = (globalSettings[resourceType] ?? []) as string[];
 			const projectEntries = (projectSettings[resourceType] ?? []) as string[];
-			this.resolveLocalEntries(
-				globalEntries,
-				resourceType,
-				target,
-				{
-					source: "local",
-					scope: "user",
-					origin: "top-level",
-				},
-				globalBaseDir,
-			);
 			this.resolveLocalEntries(
 				projectEntries,
 				resourceType,
@@ -764,6 +753,17 @@ export class DefaultPackageManager implements PackageManager {
 				},
 				projectBaseDir,
 			);
+			this.resolveLocalEntries(
+				globalEntries,
+				resourceType,
+				target,
+				{
+					source: "local",
+					scope: "user",
+					origin: "top-level",
+				},
+				globalBaseDir,
+			);
 		}
 
 		this.addAutoDiscoveredResources(accumulator, globalSettings, projectSettings, globalBaseDir, projectBaseDir);
@@ -1600,35 +1600,6 @@ export class DefaultPackageManager implements PackageManager {
 			}
 		};
 
-		addResources(
-			"extensions",
-			collectAutoExtensionEntries(userDirs.extensions),
-			userMetadata,
-			userOverrides.extensions,
-			globalBaseDir,
-		);
-		addResources(
-			"skills",
-			[...collectAutoSkillEntries(userDirs.skills), ...collectAutoSkillEntries(userAgentsSkillsDir)],
-			userMetadata,
-			userOverrides.skills,
-			globalBaseDir,
-		);
-		addResources(
-			"prompts",
-			collectAutoPromptEntries(userDirs.prompts),
-			userMetadata,
-			userOverrides.prompts,
-			globalBaseDir,
-		);
-		addResources(
-			"themes",
-			collectAutoThemeEntries(userDirs.themes),
-			userMetadata,
-			userOverrides.themes,
-			globalBaseDir,
-		);
-
 		addResources(
 			"extensions",
 			collectAutoExtensionEntries(projectDirs.extensions),
@@ -1660,6 +1631,35 @@ export class DefaultPackageManager implements PackageManager {
 			projectOverrides.themes,
 			projectBaseDir,
 		);
+
+		addResources(
+			"extensions",
+			collectAutoExtensionEntries(userDirs.extensions),
+			userMetadata,
+			userOverrides.extensions,
+			globalBaseDir,
+		);
+		addResources(
+			"skills",
+			[...collectAutoSkillEntries(userDirs.skills), ...collectAutoSkillEntries(userAgentsSkillsDir)],
+			userMetadata,
+			userOverrides.skills,
+			globalBaseDir,
+		);
+		addResources(
+			"prompts",
+			collectAutoPromptEntries(userDirs.prompts),
+			userMetadata,
+			userOverrides.prompts,
+			globalBaseDir,
+		);
+		addResources(
+			"themes",
+			collectAutoThemeEntries(userDirs.themes),
+			userMetadata,
+			userOverrides.themes,
+			globalBaseDir,
+		);
 	}
 
 	private collectFilesFromPaths(paths: string[], resourceType: ResourceType): string[] {

packages/coding-agent/src/core/resource-loader.ts

@@ -384,13 +384,10 @@ export class DefaultResourceLoader implements ResourceLoader {
 		extensionsResult.errors.push(...inlineExtensions.errors);
 
 		// Detect extension conflicts (tools, commands, flags with same names from different extensions)
+		// Keep all extensions loaded. Conflicts are reported as diagnostics, and precedence is handled by load order.
 		const conflicts = this.detectExtensionConflicts(extensionsResult.extensions);
-		if (conflicts.length > 0) {
-			const conflictingPaths = new Set(conflicts.map((c) => c.path));
-			extensionsResult.extensions = extensionsResult.extensions.filter((ext) => !conflictingPaths.has(ext.path));
-			for (const conflict of conflicts) {
-				extensionsResult.errors.push({ path: conflict.path, error: conflict.message });
-			}
+		for (const conflict of conflicts) {
+			extensionsResult.errors.push({ path: conflict.path, error: conflict.message });
 		}
 
 		this.extensionsResult = this.extensionsOverride ? this.extensionsOverride(extensionsResult) : extensionsResult;

packages/coding-agent/src/modes/interactive/interactive-mode.ts

@@ -729,7 +729,7 @@ export class InteractiveMode {
 			}
 		}
 
-		return [groups.user, groups.project, groups.path].filter(
+		return [groups.project, groups.user, groups.path].filter(
 			(group) => group.paths.length > 0 || group.packages.size > 0,
 		);
 	}

packages/coding-agent/test/extensions-runner.test.ts

@@ -234,6 +234,42 @@ describe("ExtensionRunner", () => {
 			expect(tools.length).toBe(2);
 			expect(tools.map((t) => t.definition.name).sort()).toEqual(["tool_a", "tool_b"]);
 		});
+
+		it("keeps first tool when two extensions register the same name", async () => {
+			const first = `
+				import { Type } from "@sinclair/typebox";
+				export default function(pi) {
+					pi.registerTool({
+						name: "shared",
+						label: "shared",
+						description: "first",
+						parameters: Type.Object({}),
+						execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+					});
+				}
+			`;
+			const second = `
+				import { Type } from "@sinclair/typebox";
+				export default function(pi) {
+					pi.registerTool({
+						name: "shared",
+						label: "shared",
+						description: "second",
+						parameters: Type.Object({}),
+						execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+					});
+				}
+			`;
+			fs.writeFileSync(path.join(extensionsDir, "a-first.ts"), first);
+			fs.writeFileSync(path.join(extensionsDir, "b-second.ts"), second);
+
+			const result = await discoverAndLoadExtensions([], tempDir, tempDir);
+			const runner = new ExtensionRunner(result.extensions, result.runtime, tempDir, sessionManager, modelRegistry);
+			const tools = runner.getAllRegisteredTools();
+
+			expect(tools).toHaveLength(1);
+			expect(tools[0]?.definition.description).toBe("first");
+		});
 	});
 
 	describe("command collection", () => {
@@ -377,6 +413,36 @@ describe("ExtensionRunner", () => {
 			expect(flags.has("my-flag")).toBe(true);
 		});
 
+		it("keeps first flag when two extensions register the same name", async () => {
+			const first = `
+				export default function(pi) {
+					pi.registerFlag("shared-flag", {
+						description: "first",
+						type: "boolean",
+						default: true,
+					});
+				}
+			`;
+			const second = `
+				export default function(pi) {
+					pi.registerFlag("shared-flag", {
+						description: "second",
+						type: "boolean",
+						default: false,
+					});
+				}
+			`;
+			fs.writeFileSync(path.join(extensionsDir, "a-first.ts"), first);
+			fs.writeFileSync(path.join(extensionsDir, "b-second.ts"), second);
+
+			const result = await discoverAndLoadExtensions([], tempDir, tempDir);
+			const runner = new ExtensionRunner(result.extensions, result.runtime, tempDir, sessionManager, modelRegistry);
+			const flags = runner.getFlags();
+
+			expect(flags.get("shared-flag")?.description).toBe("first");
+			expect(result.runtime.flagValues.get("shared-flag")).toBe(true);
+		});
+
 		it("can set flag values", async () => {
 			const extCode = `
 				export default function(pi) {

packages/coding-agent/test/resource-loader.test.ts

@@ -1,8 +1,12 @@
-import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { mkdirSync, readFileSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { AuthStorage } from "../src/core/auth-storage.js";
+import { ExtensionRunner } from "../src/core/extensions/runner.js";
+import { ModelRegistry } from "../src/core/model-registry.js";
 import { DefaultResourceLoader } from "../src/core/resource-loader.js";
+import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
 import type { Skill } from "../src/core/skills.js";
 
@@ -91,6 +95,126 @@ Prompt content.`,
 			expect(prompts.some((p) => p.name === "test-prompt")).toBe(true);
 		});
 
+		it("should prefer project resources over user on name collisions", async () => {
+			const userPromptsDir = join(agentDir, "prompts");
+			const projectPromptsDir = join(cwd, ".pi", "prompts");
+			mkdirSync(userPromptsDir, { recursive: true });
+			mkdirSync(projectPromptsDir, { recursive: true });
+			const userPromptPath = join(userPromptsDir, "commit.md");
+			const projectPromptPath = join(projectPromptsDir, "commit.md");
+			writeFileSync(userPromptPath, "User prompt");
+			writeFileSync(projectPromptPath, "Project prompt");
+
+			const userSkillDir = join(agentDir, "skills", "collision-skill");
+			const projectSkillDir = join(cwd, ".pi", "skills", "collision-skill");
+			mkdirSync(userSkillDir, { recursive: true });
+			mkdirSync(projectSkillDir, { recursive: true });
+			const userSkillPath = join(userSkillDir, "SKILL.md");
+			const projectSkillPath = join(projectSkillDir, "SKILL.md");
+			writeFileSync(
+				userSkillPath,
+				`---
+name: collision-skill
+description: user
+---
+User skill`,
+			);
+			writeFileSync(
+				projectSkillPath,
+				`---
+name: collision-skill
+description: project
+---
+Project skill`,
+			);
+
+			const baseTheme = JSON.parse(
+				readFileSync(join(process.cwd(), "src", "modes", "interactive", "theme", "dark.json"), "utf-8"),
+			) as { name: string; vars?: Record<string, string> };
+			baseTheme.name = "collision-theme";
+			const userThemePath = join(agentDir, "themes", "collision.json");
+			const projectThemePath = join(cwd, ".pi", "themes", "collision.json");
+			mkdirSync(join(agentDir, "themes"), { recursive: true });
+			mkdirSync(join(cwd, ".pi", "themes"), { recursive: true });
+			writeFileSync(userThemePath, JSON.stringify(baseTheme, null, 2));
+			if (baseTheme.vars) {
+				baseTheme.vars.accent = "#ff00ff";
+			}
+			writeFileSync(projectThemePath, JSON.stringify(baseTheme, null, 2));
+
+			const loader = new DefaultResourceLoader({ cwd, agentDir });
+			await loader.reload();
+
+			const prompt = loader.getPrompts().prompts.find((p) => p.name === "commit");
+			expect(prompt?.filePath).toBe(projectPromptPath);
+
+			const skill = loader.getSkills().skills.find((s) => s.name === "collision-skill");
+			expect(skill?.filePath).toBe(projectSkillPath);
+
+			const theme = loader.getThemes().themes.find((t) => t.name === "collision-theme");
+			expect(theme?.sourcePath).toBe(projectThemePath);
+		});
+
+		it("should keep both extensions loaded when command names collide", async () => {
+			const userExtDir = join(agentDir, "extensions");
+			const projectExtDir = join(cwd, ".pi", "extensions");
+			mkdirSync(userExtDir, { recursive: true });
+			mkdirSync(projectExtDir, { recursive: true });
+
+			writeFileSync(
+				join(projectExtDir, "project.ts"),
+				`export default function(pi) {
+	pi.registerCommand("deploy", {
+		description: "project deploy",
+		handler: async () => {},
+	});
+	pi.registerCommand("project-only", {
+		description: "project only",
+		handler: async () => {},
+	});
+}`,
+			);
+
+			writeFileSync(
+				join(userExtDir, "user.ts"),
+				`export default function(pi) {
+	pi.registerCommand("deploy", {
+		description: "user deploy",
+		handler: async () => {},
+	});
+	pi.registerCommand("user-only", {
+		description: "user only",
+		handler: async () => {},
+	});
+}`,
+			);
+
+			const loader = new DefaultResourceLoader({ cwd, agentDir });
+			await loader.reload();
+
+			const extensionsResult = loader.getExtensions();
+			expect(extensionsResult.extensions).toHaveLength(2);
+			expect(extensionsResult.errors.some((e) => e.error.includes('Command "/deploy" conflicts'))).toBe(true);
+
+			const sessionManager = SessionManager.inMemory();
+			const authStorage = AuthStorage.create(join(tempDir, "auth.json"));
+			const modelRegistry = new ModelRegistry(authStorage);
+			const runner = new ExtensionRunner(
+				extensionsResult.extensions,
+				extensionsResult.runtime,
+				cwd,
+				sessionManager,
+				modelRegistry,
+			);
+
+			expect(runner.getCommand("deploy")?.description).toBe("project deploy");
+			expect(runner.getCommand("project-only")?.description).toBe("project only");
+			expect(runner.getCommand("user-only")?.description).toBe("user only");
+
+			const commandNames = runner.getRegisteredCommands().map((c) => c.name);
+			expect(commandNames.filter((name) => name === "deploy")).toHaveLength(1);
+		});
+
 		it("should honor overrides for auto-discovered resources", async () => {
 			const settingsManager = SettingsManager.inMemory();
 			settingsManager.setExtensionPaths(["-extensions/disabled.ts"]);