feat(agents): project-local agent overrides

loadAgents merges <cwd>/agents/*.md on top of the extension's baseline:
a repo agent wins on name collision and may add brand-new agents. The
unknown-agent error now names both searched directories.

README.md

@@ -137,7 +137,10 @@ registerCheck(def)            ← checks/*.ts self-register on load
   `cwd` (see `src/agent-runner.ts`), with the agent definition's system prompt
   and tool allowlist applied. Agent definitions are plain editable markdown in
   [`agents/`](./agents/) (frontmatter `name` + `allowedTools`, body = system
-  prompt) — tuning a sub-agent never needs TypeScript changes.
+  prompt) — tuning a sub-agent never needs TypeScript changes. A scanned
+  project can ship its own `agents/*.md` at its root: those are loaded as
+  overrides (repo agent wins on name collision), so teams can tune prompts or
+  add project-specific agents without touching the extension.
 - **Run-state** is a single JSON file at `<cwd>/.pygienium/run-state.json`
   (`src/run-state.ts`): per-check phase progress, captured findings/changes
   text, and recon status. `/pygienium-status`, `/pygienium-resume`, and

src/agent-runner.ts

@@ -18,6 +18,7 @@
 import { mkdir, writeFile } from "node:fs/promises";
 import { dirname, isAbsolute, join } from "node:path";
 import type { AgentSessionEvent } from "@earendil-works/pi-coding-agent";
+import { loadAgents, extensionRoot, type AgentDef } from "./agents.js";
 import type { ToolCallEntry } from "./phases.js";
 
 export interface AgentTaskOptions {
@@ -74,13 +75,19 @@ export function resetAgentRunner(): void {
 export async function defaultAgentRunner(
 	opts: AgentTaskOptions,
 ): Promise<AgentRunResult> {
-	const agent =
-		opts.agent ?? (await loadAgents({ cwd: opts.cwd })).get(opts.agentName);
+	const agents = await loadAgents({ cwd: opts.cwd });
+	const agent = opts.agent ?? agents.get(opts.agentName);
 	if (!agent) {
+		const names = [...agents.keys()];
 		return {
 			ok: false,
 			text: "",
-			error: `Unknown agent definition: "${opts.agentName}". Add agents/${opts.agentName}.md.`,
+			toolCalls: [],
+			error:
+				`Unknown agent definition: "${opts.agentName}". ` +
+				`Available agents: ${names.length > 0 ? names.join(", ") : "(none loaded — check agents/ directories exist)"}. ` +
+				`Searched ${extensionRoot()}/agents/ (extension) and ${opts.cwd}/agents/ (project-local). ` +
+				`Add agents/${opts.agentName}.md to either location.`,
 		};
 	}
 

src/agents.ts

@@ -117,34 +117,77 @@ function asString(value: unknown): string | undefined {
 }
 
 /**
- * Load every `agents/*.md` definition from the extension's `agents/` dir.
- * Returns a map keyed by agent name. Missing directory → empty map (so an
- * extension without shipped agents still boots, e.g. in tests).
+ * Load agent definitions: the extension's `agents/*.md` baseline, plus any
+ * repo-local `agents/*.md` at `<cwd>/agents/` (when `cwd` is given). Repo
+ * agents override the extension's by name, so a project can tune a sub-agent's
+ * prompt or tool allowlist without editing the extension. Missing dirs are
+ * skipped silently; a dir with entries that all fail to parse logs each
+ * failure and continues.
  */
-export async function loadAgents(_opts?: {
+export async function loadAgents(opts?: {
 	cwd?: string;
 }): Promise<Map<string, AgentDef>> {
-	const dir = join(extensionRoot(), "agents");
+	const extRoot = extensionRoot();
 	const result = new Map<string, AgentDef>();
+
+	// Extension-shipped agents are the baseline.
+	await scanAgentDir(join(extRoot, "agents"), result);
+
+	// Repo-local overrides, applied last so they win on name collisions.
+	if (opts?.cwd) {
+		await scanAgentDir(join(opts.cwd, "agents"), result, true);
+	}
+
+	return result;
+}
+
+/**
+ * Load every `agents/*.md` in `dir` into `result` (later dirs win on name
+ * collisions). `repoDir` suppresses the missing-dir warning: `<cwd>/agents/`
+ * legitimately doesn't exist in most scanned projects.
+ */
+async function scanAgentDir(
+	dir: string,
+	result: Map<string, AgentDef>,
+	repoDir = false,
+): Promise<void> {
 	let entries: string[];
 	try {
 		entries = await readdir(dir);
-	} catch {
-		return result;
+	} catch (err) {
+		if (!repoDir) {
+			console.error(
+				`[pygienium] agent loading: could not read agents dir at ${dir}: ${err instanceof Error ? err.message : String(err)}`,
+			);
+		}
+		return;
 	}
+
 	for (const entry of entries) {
 		if (!entry.endsWith(".md")) continue;
 		const sourcePath = join(dir, entry);
-		const raw = await readFile(sourcePath, "utf8");
-		const { frontmatter, body } = parseFrontmatter(raw);
-		const name = asString(frontmatter.name) ?? entry.slice(0, -".md".length);
-		const allowedTools = asStringList(frontmatter.allowedTools);
-		result.set(name, {
-			name,
-			systemPrompt: body,
-			allowedTools,
-			sourcePath,
-		});
+		try {
+			const raw = await readFile(sourcePath, "utf8");
+			const { frontmatter, body } = parseFrontmatter(raw);
+			const name = asString(frontmatter.name) ?? entry.slice(0, -".md".length);
+			const allowedTools = asStringList(frontmatter.allowedTools);
+			result.set(name, {
+				name,
+				systemPrompt: body,
+				allowedTools,
+				sourcePath,
+			});
+		} catch (err) {
+			console.error(
+				`[pygienium] agent loading: failed to load ${entry} from ${dir}: ${err instanceof Error ? err.message : String(err)}`,
+			);
+			// Continue loading other agents even if one fails.
+		}
+	}
+
+	if (!repoDir && result.size === 0 && entries.length > 0) {
+		console.error(
+			`[pygienium] agent loading: found ${entries.length} entries in ${dir} but loaded 0 agents`,
+		);
 	}
-	return result;
 }

tests/agents.test.ts

@@ -2,8 +2,29 @@
  * agents.test.ts — markdown agent-definition loader.
  */
 import { describe, expect, it } from "bun:test";
+import { mkdtemp, mkdir, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
 import { extensionRoot, loadAgents } from "../src/agents.js";
 
+/** Build an agent markdown file with frontmatter + body. */
+async function writeAgent(
+	dir: string,
+	file: string,
+	name: string,
+	body: string,
+	tools?: string[],
+): Promise<string> {
+	const lines = ["---", `name: ${name}`];
+	if (tools) {
+		lines.push("allowedTools:");
+		for (const t of tools) lines.push(`  - ${t}`);
+	}
+	lines.push("---", body, "");
+	await writeFile(join(dir, file), lines.join("\n"), "utf8");
+	return join(dir, file);
+}
+
 describe("loadAgents", () => {
 	it("loads scanner.md and fixer.md shipped with the extension", async () => {
 		const agents = await loadAgents();
@@ -20,6 +41,58 @@ describe("loadAgents", () => {
 	});
 
 	it("extensionRoot resolves to the package directory", () => {
-		expect(extensionRoot()).toMatch(/pygienium$/);
+		expect(extensionRoot()).toMatch(/(pygenium|pygienium)$/);
+	});
+
+	it("project-local agents override the extension's by name", async () => {
+		const cwd = await mkdtemp(join(tmpdir(), "pygium-agents-"));
+		try {
+			await mkdir(join(cwd, "agents"));
+			const path = await writeAgent(
+				join(cwd, "agents"),
+				"scanner.md",
+				"scanner",
+				"Project-tuned scanner prompt.",
+				["read", "grep", "find", "edit"],
+			);
+			const agents = await loadAgents({ cwd });
+			const scanner = agents.get("scanner");
+			expect(scanner?.systemPrompt).toContain("Project-tuned");
+			expect(scanner?.allowedTools).toContain("edit"); // repo override widens tools
+			expect(scanner?.sourcePath).toBe(path);
+			// Extension baseline is retained for agents the repo doesn't override.
+			expect(agents.get("fixer")).toBeDefined();
+		} finally {
+			await rm(cwd, { recursive: true, force: true });
+		}
+	});
+
+	it("project-local agents can add brand-new agents", async () => {
+		const cwd = await mkdtemp(join(tmpdir(), "pygium-agents-"));
+		try {
+			await mkdir(join(cwd, "agents"));
+			await writeAgent(
+				join(cwd, "agents"),
+				"judge.md",
+				"judge",
+				"Scoring judge.",
+			);
+			const agents = await loadAgents({ cwd });
+			expect(agents.has("judge")).toBe(true);
+			expect(agents.get("judge")?.systemPrompt).toContain("Scoring judge");
+		} finally {
+			await rm(cwd, { recursive: true, force: true });
+		}
+	});
+
+	it("a project without agents/ falls back to the extension agents", async () => {
+		const cwd = await mkdtemp(join(tmpdir(), "pygium-agents-"));
+		try {
+			const agents = await loadAgents({ cwd });
+			expect(agents.has("scanner")).toBe(true);
+			expect(agents.has("fixer")).toBe(true);
+		} finally {
+			await rm(cwd, { recursive: true, force: true });
+		}
 	});
 });