feat(coding-agent): add tool override support via extensions

- Add setActiveTools() to ExtensionAPI for dynamic tool management
- Extensions can now override, wrap, or disable built-in tools
- Add tool-override.ts example demonstrating the pattern
- Update documentation for tool override capabilities

packages/coding-agent/src/cli/args.ts

@@ -90,24 +90,18 @@ export function parseArgs(args: string[], extensionFlags?: Map<string, { type: "
 		} else if (arg === "--no-tools") {
 			result.noTools = true;
 		} else if (arg === "--tools" && i + 1 < args.length) {
-			const toolsArg = args[++i];
-			// Handle empty string as no tools (e.g., --tools '')
-			if (toolsArg === "") {
-				result.tools = [];
-			} else {
-				const toolNames = toolsArg.split(",").map((s) => s.trim());
-				const validTools: ToolName[] = [];
-				for (const name of toolNames) {
-					if (name in allTools) {
-						validTools.push(name as ToolName);
-					} else {
-						console.error(
-							chalk.yellow(`Warning: Unknown tool "${name}". Valid tools: ${Object.keys(allTools).join(", ")}`),
-						);
-					}
+			const toolNames = args[++i].split(",").map((s) => s.trim());
+			const validTools: ToolName[] = [];
+			for (const name of toolNames) {
+				if (name in allTools) {
+					validTools.push(name as ToolName);
+				} else {
+					console.error(
+						chalk.yellow(`Warning: Unknown tool "${name}". Valid tools: ${Object.keys(allTools).join(", ")}`),
+					);
 				}
-				result.tools = validTools;
 			}
+			result.tools = validTools;
 		} else if (arg === "--thinking" && i + 1 < args.length) {
 			const level = args[++i];
 			if (isValidThinkingLevel(level)) {
@@ -188,7 +182,7 @@ ${chalk.bold("Options:")}
                                  Available: read, bash, edit, write, grep, find, ls
   --thinking <level>             Set thinking level: off, minimal, low, medium, high, xhigh
   --extension, -e <path>         Load an extension file (can be used multiple times)
-  --no-extensions                Disable extensions discovery and loading
+  --no-extensions                Disable extension discovery (explicit -e paths still work)
   --no-skills                    Disable skills discovery and loading
   --skills <patterns>            Comma-separated glob patterns to filter skills (e.g., git-*,docker)
   --export <file>                Export session file to HTML and exit

packages/coding-agent/src/core/sdk.ts

@@ -514,7 +514,10 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 	}
 
 	// Initially active tools = active built-in + extension tools
-	let activeToolsArray: Tool[] = [...initialActiveBuiltInTools, ...wrappedExtensionTools];
+	// Extension tools can override built-in tools with the same name
+	const extensionToolNames = new Set(wrappedExtensionTools.map((t) => t.name));
+	const nonOverriddenBuiltInTools = initialActiveBuiltInTools.filter((t) => !extensionToolNames.has(t.name));
+	let activeToolsArray: Tool[] = [...nonOverriddenBuiltInTools, ...wrappedExtensionTools];
 	time("combineTools");
 
 	// Wrap tools with extensions if available

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

@@ -222,12 +222,6 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 	const hasLs = tools.includes("ls");
 	const hasRead = tools.includes("read");
 
-	// Read-only mode notice (only if we have some read-only tools but no write tools)
-	// Skip this if there are no built-in tools at all (extensions may provide write capabilities)
-	if (tools.length > 0 && !hasBash && !hasEdit && !hasWrite) {
-		guidelinesList.push("You are in READ-ONLY mode - you cannot modify files or execute arbitrary commands");
-	}
-
 	// Bash without edit/write = read-only bash mode
 	if (hasBash && !hasEdit && !hasWrite) {
 		guidelinesList.push(
@@ -266,9 +260,7 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 
 	// Always include these
 	guidelinesList.push("Be concise in your responses");
-	if (tools.length > 0) {
-		guidelinesList.push("Show file paths clearly when working with files");
-	}
+	guidelinesList.push("Show file paths clearly when working with files");
 
 	const guidelines = guidelinesList.map((g) => `- ${g}`).join("\n");