feat(cli): auto-upgrade skill and clean legacy hooks on start/restart

[Marvae]

• Add runUpgradeMigrations() called from start/restart commands so npm update + teams-bot restart completes an upgrade automatically
• syncInstalledSkill: version-stamped sync — only replaces the installed skill directory when the package version changes (.version marker)
• cleanupLegacyHooks: removes stale SessionStart hook configs from settings.json that referenced the now-deleted session-start.sh
• Move skill template from .claude/skills/ to skills/ so it won't be auto-discovered by Claude Code as a live skill
• Remove stale .claude/hooks/ from package.json files array
• Remove scope choice from install-skill (always installs globally)
• Fix scope "2" destination path (was using projectDir instead of cwd)
• Deduplicate cleanupLegacyHooks from uninstallSkill into shared function

[Copilot]

Pull request overview

This PR adds automatic upgrade behavior to the CLI so bot start/restart can migrate user config and keep the bundled /handoff skill in sync after package updates.

Changes:

• Add runUpgradeMigrations() and invoke it from start/restart to perform upgrade-time maintenance.
• Implement migrations to (1) remove legacy SessionStart hook configs referencing session-start.sh and (2) version-stamp + sync the installed /handoff skill directory only when the package version changes.
• Move the packaged skill template to skills/handoff/ and update package.json publish contents accordingly; add Vitest coverage for migrations.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/upgrade-migrations.test.ts	Adds test coverage for legacy hook cleanup and version-stamped skill sync behavior.
src/cli/skill.ts	Implements migrations (cleanupLegacyHooks, syncInstalledSkill) and updates install logic to use the new skills/ template location.
src/cli/commands.ts	Calls migrations on start and restart to make upgrades automatic.
skills/handoff/SKILL.md	Introduces the new packaged skill template location/content.
package.json	Updates published files list to include skills/ and remove legacy .claude/... entries.

Comments suppressed due to low confidence (1)

src/cli/commands.ts:187

• runUpgradeMigrations() is executed before the healthz probe in startCommand(). If a migration throws (e.g., due to unexpected settings.json shape or filesystem permissions), the CLI will fail even when the bot is already running. Consider making migrations non-fatal (catch/log) so teams-bot start remains reliable.

export async function startCommand(): Promise<void> {
  const platform = detectPlatform();
  runUpgradeMigrations();

  // Check if already running
  if (await probe("http://127.0.0.1:3978/healthz", 2000)) {
    console.log("Bot is already running.");

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[Copilot]

This test case name is misleading: the second SessionStart group uses a command containing "session-start.sh", which the migration intentionally removes. Consider renaming the test to reflect that it preserves hooks not matching the legacy session-start.sh pattern, rather than implying session-start.sh is non-legacy.

[Copilot]

cleanupLegacyHooks assumes hooks.SessionStart is an array and immediately calls .filter() on it. If a user’s settings.json has SessionStart set to a non-array value (e.g., an object/string), this will throw and can break start/restart (since migrations now run automatically). Add an Array.isArray(hooks.SessionStart) guard and skip (or normalize) when the shape is unexpected.

Suggested change

	if (!hooks?.SessionStart) continue;
	const groups = hooks.SessionStart as Array<Record<string, unknown>>;
	const sessionStart = hooks?.SessionStart;
	if (!Array.isArray(sessionStart)) continue;
	const groups = sessionStart as Array<Record<string, unknown>>;

[Copilot]

copyDirSync is documented as replacing the destination directory contents with the source directory contents, but the implementation only copies top-level files and skips subdirectories. Either make this a recursive directory copy (so future skill templates with nested files work) or update the doc/comment + name to reflect that only flat files are copied.

Suggested change

	if (!entry.isFile()) continue;
	fs.copyFileSync(path.join(srcDir, entry.name), path.join(destDir, entry.name));
	const srcPath = path.join(srcDir, entry.name);
	const destPath = path.join(destDir, entry.name);
	if (entry.isDirectory()) {
	copyDirSync(srcPath, destPath);
	continue;
	}
	if (!entry.isFile()) continue;
	fs.copyFileSync(srcPath, destPath);

[Copilot]

runUpgradeMigrations() now runs as part of restartCommand(). Since it performs filesystem reads/writes, any thrown error will abort the restart flow before stopService/startService runs. Consider wrapping migrations in a try/catch here (or inside runUpgradeMigrations) and logging a warning so restart remains best-effort.

Suggested change

	runUpgradeMigrations();
	try {
	await Promise.resolve(runUpgradeMigrations());
	} catch (error) {
	console.warn(
	"Warning: upgrade migrations failed during restart; continuing with service restart.",
	error,
	);
	}