fix(prompting): preserved CLI prompt precedence over SYSTEM.md

Skip the secondary loadSystemPromptFiles capability walk when the caller already controls block 0 via customPrompt/resolvedCustomPrompt, so project/user SYSTEM.md cannot silently augment a CLI --system-prompt override.

Fixes #3014

packages/coding-agent/src/system-prompt.ts

@@ -505,9 +505,15 @@ export async function buildSystemPrompt(options: BuildSystemPromptOptions = {}):
 		return result.value;
 	}
 
-	const systemPromptCustomizationPromise = logger.time("loadSystemPromptFiles", loadSystemPromptFiles, {
-		cwd: resolvedCwd,
-	});
+	// Caller-supplied `customPrompt` / `resolvedCustomPrompt` owns block 0; the
+	// secondary capability-path `SYSTEM.md` walk-up MUST NOT silently augment it,
+	// because that would defeat CLI precedence over project/user `SYSTEM.md`.
+	const callerControlsCustomPrompt =
+		(typeof providedResolvedCustomPrompt === "string" && providedResolvedCustomPrompt.length > 0) ||
+		(typeof customPrompt === "string" && customPrompt.length > 0);
+	const systemPromptCustomizationPromise: Promise<string | null> = callerControlsCustomPrompt
+		? Promise.resolve(null)
+		: logger.time("loadSystemPromptFiles", loadSystemPromptFiles, { cwd: resolvedCwd });
 	const contextFilesPromise = providedContextFiles
 		? Promise.resolve(providedContextFiles)
 		: logger.time("loadProjectContextFiles", loadProjectContextFiles, { cwd: resolvedCwd });

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

@@ -106,6 +106,33 @@ describe("SYSTEM.md prompt assembly", () => {
 		expect(promptText).not.toContain("File content that must not replace the prompt.");
 	});
 
+	it("suppresses discovered SYSTEM.md when the caller supplies a custom prompt", async () => {
+		const projectDir = path.join(tempDir, "project");
+		fs.mkdirSync(path.join(projectDir, ".omp"), { recursive: true });
+		fs.writeFileSync(path.join(projectDir, ".omp", "SYSTEM.md"), "Discovered project SYSTEM prompt");
+
+		const { systemPrompt } = await buildSystemPrompt({
+			cwd: projectDir,
+			resolvedCustomPrompt: "CLI custom prompt",
+			contextFiles: [],
+			skills: [],
+			rules: [],
+			toolNames: ["read"],
+			tools: READ_TOOL,
+			workspaceTree: {
+				rootPath: projectDir,
+				rendered: "",
+				truncated: false,
+				totalLines: 0,
+				agentsMdFiles: [],
+			},
+		});
+
+		const promptText = systemPrompt.join("\n\n");
+		expect(promptText).toContain("CLI custom prompt");
+		expect(promptText).not.toContain("Discovered project SYSTEM prompt");
+	});
+
 	it("prefers project SYSTEM.md over user SYSTEM.md", async () => {
 		const projectDir = path.join(tempDir, "project");
 		fs.mkdirSync(path.join(projectDir, ".omp"), { recursive: true });