diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index 5890ec6c..39c2751d 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -118,6 +118,24 @@ interface ResourceAccumulator {
 	themes: Map<string, { metadata: PathMetadata; enabled: boolean }>;
 }
 
+/**
+ * Compute a numeric precedence rank for a resource based on its metadata.
+ * Lower rank = higher precedence. Used to sort resolved resources so that
+ * name-collision resolution ("first wins") produces the correct outcome.
+ *
+ * Precedence (highest to lowest):
+ *   0  project + settings entry (source: "local", scope: "project")
+ *   1  project + auto-discovered (source: "auto", scope: "project")
+ *   2  user + settings entry (source: "local", scope: "user")
+ *   3  user + auto-discovered (source: "auto", scope: "user")
+ *   4  package resource (origin: "package")
+ */
+function resourcePrecedenceRank(m: PathMetadata): number {
+	if (m.origin === "package") return 4;
+	const scopeBase = m.scope === "project" ? 0 : 2;
+	return scopeBase + (m.source === "local" ? 0 : 1);
+}
+
 interface PackageFilter {
 	extensions?: string[];
 	skills?: string[];
@@ -2146,11 +2164,13 @@ export class DefaultPackageManager implements PackageManager {
 
 	private toResolvedPaths(accumulator: ResourceAccumulator): ResolvedPaths {
 		const toResolved = (entries: Map<string, { metadata: PathMetadata; enabled: boolean }>): ResolvedResource[] => {
-			return Array.from(entries.entries()).map(([path, { metadata, enabled }]) => ({
+			const resolved = Array.from(entries.entries()).map(([path, { metadata, enabled }]) => ({
 				path,
 				enabled,
 				metadata,
 			}));
+			resolved.sort((a, b) => resourcePrecedenceRank(a.metadata) - resourcePrecedenceRank(b.metadata));
+			return resolved;
 		};
 
 		return {
diff --git a/packages/coding-agent/src/core/resource-loader.ts b/packages/coding-agent/src/core/resource-loader.ts
index 095cf870..9450c9ed 100644
--- a/packages/coding-agent/src/core/resource-loader.ts
+++ b/packages/coding-agent/src/core/resource-loader.ts
@@ -413,7 +413,7 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		const skillPaths = this.noSkills
 			? this.mergePaths(cliEnabledSkills, this.additionalSkillPaths)
-			: this.mergePaths([...enabledSkills, ...cliEnabledSkills], this.additionalSkillPaths);
+			: this.mergePaths([...cliEnabledSkills, ...enabledSkills], this.additionalSkillPaths);
 
 		this.lastSkillPaths = skillPaths;
 		this.updateSkillsFromPaths(skillPaths, metadataByPath);
@@ -425,7 +425,7 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		const promptPaths = this.noPromptTemplates
 			? this.mergePaths(cliEnabledPrompts, this.additionalPromptTemplatePaths)
-			: this.mergePaths([...enabledPrompts, ...cliEnabledPrompts], this.additionalPromptTemplatePaths);
+			: this.mergePaths([...cliEnabledPrompts, ...enabledPrompts], this.additionalPromptTemplatePaths);
 
 		this.lastPromptPaths = promptPaths;
 		this.updatePromptsFromPaths(promptPaths, metadataByPath);
@@ -437,7 +437,7 @@ export class DefaultResourceLoader implements ResourceLoader {
 
 		const themePaths = this.noThemes
 			? this.mergePaths(cliEnabledThemes, this.additionalThemePaths)
-			: this.mergePaths([...enabledThemes, ...cliEnabledThemes], this.additionalThemePaths);
+			: this.mergePaths([...cliEnabledThemes, ...enabledThemes], this.additionalThemePaths);
 
 		this.lastThemePaths = themePaths;
 		this.updateThemesFromPaths(themePaths, metadataByPath);
diff --git a/packages/coding-agent/test/suite/regressions/2781-skill-collision-precedence.test.ts b/packages/coding-agent/test/suite/regressions/2781-skill-collision-precedence.test.ts
new file mode 100644
index 00000000..e7e17f58
--- /dev/null
+++ b/packages/coding-agent/test/suite/regressions/2781-skill-collision-precedence.test.ts
@@ -0,0 +1,120 @@
+import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { DefaultResourceLoader } from "../../../src/core/resource-loader.js";
+
+describe("issue #2781 skill collision precedence: user skills should override package skills", () => {
+	let tempDir: string;
+	let agentDir: string;
+	let cwd: string;
+
+	beforeEach(() => {
+		tempDir = join(tmpdir(), `pi-2781-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+		agentDir = join(tempDir, "agent");
+		cwd = join(tempDir, "project");
+		mkdirSync(agentDir, { recursive: true });
+		mkdirSync(cwd, { recursive: true });
+	});
+
+	afterEach(() => {
+		rmSync(tempDir, { recursive: true, force: true });
+	});
+
+	function createPackageWithSkill(name: string, description: string): string {
+		const pkgDir = join(tempDir, `fake-package-${name}`);
+		const skillDir = join(pkgDir, "skills", name);
+		mkdirSync(skillDir, { recursive: true });
+		writeFileSync(
+			join(pkgDir, "package.json"),
+			JSON.stringify({ name: `fake-pkg-${name}`, version: "1.0.0", pi: { skills: [`skills/${name}`] } }, null, 2),
+		);
+		writeFileSync(
+			join(skillDir, "SKILL.md"),
+			`---\nname: ${name}\ndescription: ${description}\n---\nPackage skill content`,
+		);
+		return pkgDir;
+	}
+
+	function createUserSkill(name: string, description: string): string {
+		const skillDir = join(agentDir, "skills", name);
+		mkdirSync(skillDir, { recursive: true });
+		const skillPath = join(skillDir, "SKILL.md");
+		writeFileSync(skillPath, `---\nname: ${name}\ndescription: ${description}\n---\nUser skill content`);
+		return skillPath;
+	}
+
+	function createProjectSkill(name: string, description: string): string {
+		const skillDir = join(cwd, ".pi", "skills", name);
+		mkdirSync(skillDir, { recursive: true });
+		const skillPath = join(skillDir, "SKILL.md");
+		writeFileSync(skillPath, `---\nname: ${name}\ndescription: ${description}\n---\nProject skill content`);
+		return skillPath;
+	}
+
+	function createSettingsWithPackage(pkgDir: string, scope: "user" | "project"): void {
+		const settingsDir = scope === "user" ? agentDir : join(cwd, ".pi");
+		mkdirSync(settingsDir, { recursive: true });
+		writeFileSync(join(settingsDir, "settings.json"), JSON.stringify({ packages: [pkgDir] }, null, 2));
+	}
+
+	it("user auto-discovered skill should override package skill with same name", async () => {
+		const pkgDir = createPackageWithSkill("web-fetch", "Package web-fetch skill");
+		const userSkillPath = createUserSkill("web-fetch", "User web-fetch override");
+		createSettingsWithPackage(pkgDir, "user");
+
+		const loader = new DefaultResourceLoader({ cwd, agentDir });
+		await loader.reload();
+
+		const { skills } = loader.getSkills();
+		const webFetch = skills.find((s) => s.name === "web-fetch");
+		expect(webFetch).toBeDefined();
+		expect(webFetch!.filePath).toBe(userSkillPath);
+		expect(webFetch!.description).toBe("User web-fetch override");
+	});
+
+	it("project auto-discovered skill should override package skill with same name", async () => {
+		const pkgDir = createPackageWithSkill("web-fetch", "Package web-fetch skill");
+		const projectSkillPath = createProjectSkill("web-fetch", "Project web-fetch override");
+		createSettingsWithPackage(pkgDir, "user");
+
+		const loader = new DefaultResourceLoader({ cwd, agentDir });
+		await loader.reload();
+
+		const { skills } = loader.getSkills();
+		const webFetch = skills.find((s) => s.name === "web-fetch");
+		expect(webFetch).toBeDefined();
+		expect(webFetch!.filePath).toBe(projectSkillPath);
+		expect(webFetch!.description).toBe("Project web-fetch override");
+	});
+
+	it("project skill should override user skill which should override package skill", async () => {
+		const pkgDir = createPackageWithSkill("web-fetch", "Package web-fetch skill");
+		createUserSkill("web-fetch", "User web-fetch override");
+		const projectSkillPath = createProjectSkill("web-fetch", "Project web-fetch override");
+		createSettingsWithPackage(pkgDir, "user");
+
+		const loader = new DefaultResourceLoader({ cwd, agentDir });
+		await loader.reload();
+
+		const { skills } = loader.getSkills();
+		const webFetch = skills.find((s) => s.name === "web-fetch");
+		expect(webFetch).toBeDefined();
+		expect(webFetch!.filePath).toBe(projectSkillPath);
+		expect(webFetch!.description).toBe("Project web-fetch override");
+	});
+
+	it("collision diagnostics should report package skill as loser when user skill wins", async () => {
+		const pkgDir = createPackageWithSkill("web-fetch", "Package web-fetch skill");
+		createUserSkill("web-fetch", "User web-fetch override");
+		createSettingsWithPackage(pkgDir, "user");
+
+		const loader = new DefaultResourceLoader({ cwd, agentDir });
+		await loader.reload();
+
+		const { diagnostics } = loader.getSkills();
+		const collision = diagnostics.find((d) => d.type === "collision" && d.collision?.name === "web-fetch");
+		expect(collision).toBeDefined();
+		expect(collision!.collision!.loserPath).toContain("fake-package");
+	});
+});