Merge hooks and custom-tools into unified extensions system (#454)

Breaking changes:
- Settings: 'hooks' and 'customTools' arrays replaced with 'extensions'
- CLI: '--hook' and '--tool' flags replaced with '--extension' / '-e'
- API: HookMessage renamed to CustomMessage, role 'hookMessage' to 'custom'
- API: FileSlashCommand renamed to PromptTemplate
- API: discoverSlashCommands() renamed to discoverPromptTemplates()
- Directories: commands/ renamed to prompts/ for prompt templates

Migration:
- Session version bumped to 3 (auto-migrates v2 sessions)
- Old 'hookMessage' role entries converted to 'custom'

Structural changes:
- src/core/hooks/ and src/core/custom-tools/ merged into src/core/extensions/
- src/core/slash-commands.ts renamed to src/core/prompt-templates.ts
- examples/hooks/ and examples/custom-tools/ merged into examples/extensions/
- docs/hooks.md and docs/custom-tools.md merged into docs/extensions.md

New test coverage:
- test/extensions-runner.test.ts (10 tests)
- test/extensions-discovery.test.ts (26 tests)
- test/prompt-templates.test.ts

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

@@ -26,8 +26,7 @@ export interface Args {
 	sessionDir?: string;
 	models?: string[];
 	tools?: ToolName[];
-	hooks?: string[];
-	customTools?: string[];
+	extensions?: string[];
 	print?: boolean;
 	export?: string;
 	noSkills?: boolean;
@@ -35,7 +34,7 @@ export interface Args {
 	listModels?: string | true;
 	messages: string[];
 	fileArgs: string[];
-	/** Unknown flags (potentially hook flags) - map of flag name to value */
+	/** Unknown flags (potentially extension flags) - map of flag name to value */
 	unknownFlags: Map<string, boolean | string>;
 }
 
@@ -45,7 +44,7 @@ export function isValidThinkingLevel(level: string): level is ThinkingLevel {
 	return VALID_THINKING_LEVELS.includes(level as ThinkingLevel);
 }
 
-export function parseArgs(args: string[], hookFlags?: Map<string, { type: "boolean" | "string" }>): Args {
+export function parseArgs(args: string[], extensionFlags?: Map<string, { type: "boolean" | "string" }>): Args {
 	const result: Args = {
 		messages: [],
 		fileArgs: [],
@@ -114,12 +113,9 @@ export function parseArgs(args: string[], hookFlags?: Map<string, { type: "boole
 			result.print = true;
 		} else if (arg === "--export" && i + 1 < args.length) {
 			result.export = args[++i];
-		} else if (arg === "--hook" && i + 1 < args.length) {
-			result.hooks = result.hooks ?? [];
-			result.hooks.push(args[++i]);
-		} else if (arg === "--tool" && i + 1 < args.length) {
-			result.customTools = result.customTools ?? [];
-			result.customTools.push(args[++i]);
+		} else if ((arg === "--extension" || arg === "-e") && i + 1 < args.length) {
+			result.extensions = result.extensions ?? [];
+			result.extensions.push(args[++i]);
 		} else if (arg === "--no-skills") {
 			result.noSkills = true;
 		} else if (arg === "--skills" && i + 1 < args.length) {
@@ -134,18 +130,18 @@ export function parseArgs(args: string[], hookFlags?: Map<string, { type: "boole
 			}
 		} else if (arg.startsWith("@")) {
 			result.fileArgs.push(arg.slice(1)); // Remove @ prefix
-		} else if (arg.startsWith("--") && hookFlags) {
-			// Check if it's a hook-registered flag
+		} else if (arg.startsWith("--") && extensionFlags) {
+			// Check if it's an extension-registered flag
 			const flagName = arg.slice(2);
-			const hookFlag = hookFlags.get(flagName);
-			if (hookFlag) {
-				if (hookFlag.type === "boolean") {
+			const extFlag = extensionFlags.get(flagName);
+			if (extFlag) {
+				if (extFlag.type === "boolean") {
 					result.unknownFlags.set(flagName, true);
-				} else if (hookFlag.type === "string" && i + 1 < args.length) {
+				} else if (extFlag.type === "string" && i + 1 < args.length) {
 					result.unknownFlags.set(flagName, args[++i]);
 				}
 			}
-			// Unknown flags without hookFlags are silently ignored (first pass)
+			// Unknown flags without extensionFlags are silently ignored (first pass)
 		} else if (!arg.startsWith("-")) {
 			result.messages.push(arg);
 		}
@@ -178,8 +174,7 @@ ${chalk.bold("Options:")}
   --tools <tools>                Comma-separated list of tools to enable (default: read,bash,edit,write)
                                  Available: read, bash, edit, write, grep, find, ls
   --thinking <level>             Set thinking level: off, minimal, low, medium, high, xhigh
-  --hook <path>                  Load a hook file (can be used multiple times)
-  --tool <path>                  Load a custom tool file (can be used multiple times)
+  --extension, -e <path>         Load an extension file (can be used multiple times)
   --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
@@ -187,7 +182,7 @@ ${chalk.bold("Options:")}
   --help, -h                     Show this help
   --version, -v                  Show version number
 
-Hooks can register additional flags (e.g., --plan from plan-mode hook).
+Extensions can register additional flags (e.g., --plan from plan-mode extension).
 
 ${chalk.bold("Examples:")}
   # Interactive mode