feat(coding-agent): added automatic deduplication of context files by content

- Added automatic deduplication of identical context files by content, keeping the closest (lowest depth) copy when duplicates are discovered.
- Implemented dedupeExactContextFiles() function to filter duplicate context entries in both explicit and discovered file lists.
- Added 3 test cases covering deduplication of explicit context entries, discovered context entries, and preservation of distinct entries.

packages/coding-agent/test/system-prompt-dedup.test.ts

@@ -5,7 +5,11 @@ import * as path from "node:path";
 import { Settings } from "@oh-my-pi/pi-coding-agent/config/settings";
 import { createAgentSession } from "@oh-my-pi/pi-coding-agent/sdk";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { loadSystemPromptFiles } from "@oh-my-pi/pi-coding-agent/system-prompt";
+import {
+	buildSystemPrompt,
+	loadProjectContextFiles,
+	loadSystemPromptFiles,
+} from "@oh-my-pi/pi-coding-agent/system-prompt";
 
 function escapeRegExp(text: string): string {
 	return text.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
@@ -77,4 +81,62 @@ describe("SYSTEM.md prompt assembly", () => {
 
 		await expect(loadSystemPromptFiles({ cwd: projectDir })).resolves.toBe("Project SYSTEM prompt");
 	});
+	it("drops identical explicit context entries even when file names differ", async () => {
+		const farPath = path.join(tempDir, "far", "AGENTS.md");
+		const nearPath = path.join(tempDir, "near", "CLAUDE.md");
+		const sharedContent = "Shared context instructions";
+
+		const prompt = await buildSystemPrompt({
+			cwd: tempDir,
+			customPrompt: "Base prompt",
+			contextFiles: [
+				{ path: farPath, content: sharedContent, depth: 2 },
+				{ path: nearPath, content: sharedContent, depth: 0 },
+			],
+			skills: [],
+			rules: [],
+			toolNames: [],
+		});
+
+		const matches = prompt.match(new RegExp(escapeRegExp(sharedContent), "g")) ?? [];
+		expect(matches).toHaveLength(1);
+		expect(prompt).not.toContain(`<file path="${farPath}">`);
+		expect(prompt).toContain(`<file path="${nearPath}">`);
+	});
+
+	it("drops identical discovered context entries and keeps the closest copy", async () => {
+		const projectDir = path.join(tempDir, "project");
+		const appDir = path.join(projectDir, "packages", "app");
+		const sharedContent = "Shared context instructions";
+
+		fs.mkdirSync(appDir, { recursive: true });
+		fs.writeFileSync(path.join(projectDir, "AGENTS.md"), sharedContent);
+		fs.writeFileSync(path.join(appDir, "AGENTS.md"), sharedContent);
+
+		const contextFiles = await loadProjectContextFiles({ cwd: appDir });
+		const discoveredFiles = contextFiles.filter(file => file.path.startsWith(projectDir));
+
+		expect(discoveredFiles).toHaveLength(1);
+		expect(discoveredFiles[0]?.path).toBe(path.join(appDir, "AGENTS.md"));
+	});
+
+	it("keeps distinct context entries when their contents differ", async () => {
+		const farPath = path.join(tempDir, "far", "AGENTS.md");
+		const nearPath = path.join(tempDir, "near", "CLAUDE.md");
+
+		const prompt = await buildSystemPrompt({
+			cwd: tempDir,
+			customPrompt: "Base prompt",
+			contextFiles: [
+				{ path: farPath, content: "Root context instructions", depth: 2 },
+				{ path: nearPath, content: "Near context instructions", depth: 0 },
+			],
+			skills: [],
+			rules: [],
+			toolNames: [],
+		});
+
+		expect(prompt).toContain("Root context instructions");
+		expect(prompt).toContain("Near context instructions");
+	});
 });