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/core/settings-manager.ts

@@ -52,8 +52,7 @@ export interface Settings {
 	hideThinkingBlock?: boolean;
 	shellPath?: string; // Custom shell path (e.g., for Cygwin users on Windows)
 	collapseChangelog?: boolean; // Show condensed changelog after update (use /changelog for full)
-	hooks?: string[]; // Array of hook file paths
-	customTools?: string[]; // Array of custom tool file paths
+	extensions?: string[]; // Array of extension file paths
 	skills?: SkillsSettings;
 	terminal?: TerminalSettings;
 	images?: ImageSettings;
@@ -340,21 +339,12 @@ export class SettingsManager {
 		this.save();
 	}
 
-	getHookPaths(): string[] {
-		return [...(this.settings.hooks ?? [])];
+	getExtensionPaths(): string[] {
+		return [...(this.settings.extensions ?? [])];
 	}
 
-	setHookPaths(paths: string[]): void {
-		this.globalSettings.hooks = paths;
-		this.save();
-	}
-
-	getCustomToolPaths(): string[] {
-		return [...(this.settings.customTools ?? [])];
-	}
-
-	setCustomToolPaths(paths: string[]): void {
-		this.globalSettings.customTools = paths;
+	setExtensionPaths(paths: string[]): void {
+		this.globalSettings.extensions = paths;
 		this.save();
 	}