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

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,
 		);
 	}