feat(workspace): bootstrap worktrees by default (closes #50)

[chubes4]

Summary

worktree add now runs detected setup steps by default so the new checkout is immediately test/build-ready. Pass --skip-bootstrap to opt out for pure-read use. Closes #50.

# Default: bootstrapped, ready to test/build
wp datamachine-code workspace worktree add <repo> <branch>

# Opt out for a bare checkout
wp datamachine-code workspace worktree add <repo> <branch> --skip-bootstrap

Why on by default

The earlier draft of this PR shipped --bootstrap as opt-in (matching the wording in the issue). Reconsidered after discussion: worktrees are overwhelmingly created to do branch work (run tests, build, commit, push), not to read code. Read-only consumers can use the primary checkout, which is already read-only by default. Making bootstrap opt-in forces every new agent to know about the flag or they silently hit the exact trap the issue describes (vitest can't load spec, sh: nx: command not found).

Making it on-by-default with a --skip-bootstrap escape hatch mirrors the existing inject_context=true + --skip-context-injection convention for agent-memory injection from #45. Consistent mental model across worktree setup surfaces.

What bootstrap does

Three independent steps, in order, each skipped gracefully when trigger file or tool is missing:

1. git submodule update --init --recursive — if .gitmodules exists
2. Package-manager install — based on lockfile priority (pnpm > bun > yarn > npm):
   • pnpm-lock.yaml → pnpm install --frozen-lockfile
   • bun.lockb / bun.lock → bun install --frozen-lockfile
   • yarn.lock → yarn install --immutable
   • package-lock.json → npm ci
3. composer install --no-interaction --prefer-dist — if composer.lock exists

A repo with package.json but no lockfile is treated as "no package-manager step" — we never guess which manager to use.

Safety model

• Graceful degradation. Missing tool on $PATH reports skipped with a reason, not an error. Missing trigger file = skipped.
• No rollback on failure. A failed step is surfaced as FAILED in the result and shown as a CLI warning, but the worktree itself stays created so the user can retry manually. Matches the existing context_injected=false + context_skip_reason=… precedent from Inject site-agent context into worktrees on creation #45.
• No WordPress coupling. WorktreeBootstrapper is a pure class so tests/smoke-worktree-bootstrap.php exercises it without a WP bootstrap.

Output

Success: Worktree "data-machine@feat-foo" added at … (branch feat-foo).
Handle: data-machine@feat-foo
Path:   /Users/…/data-machine@feat-foo
Branch: feat-foo (created)
Context: injected (2 files)
  - …/.claude/CLAUDE.local.md
  - …/.opencode/AGENTS.local.md
Bootstrap: ok
  - submodules skipped (no .gitmodules)
  ✓ packages   ran: npm ci
  ✓ composer   ran: composer install --no-interaction --prefer-dist

Files

• New: inc/Workspace/WorktreeBootstrapper.php — detect + bootstrap + format helpers
• New: tests/smoke-worktree-bootstrap.php — 30 assertions covering detection priority, skip behavior, real-repo submodule run, failure formatting
• Modified: inc/Workspace/Workspace.php — new $bootstrap param on worktree_add() (default true)
• Modified: inc/Abilities/WorkspaceAbilities.php — bootstrap input on datamachine/workspace-worktree-add (default true) + output schema
• Modified: inc/Cli/Commands/WorkspaceCommand.php — --skip-bootstrap flag, help block, result rendering
• Modified: tests/TESTING.md — new section 3a for the CLI smoke

Testing

Pure smokes (62/62 passing):

$ php tests/smoke-worktree-bootstrap.php
30/30 passed

$ php tests/smoke-worktree-handles.php
32/32 passed

Covers: detect() priority (pnpm > bun > yarn > npm), skip on empty dir, real-repo submodule run, format() output shape (ran + failed + skipped markers, failure output tail).

Live CLI tests on intelligence-chubes4 Studio site:

Scenario	Repo	Result
Default (no flag) on Node+PHP repo	data-machine	✓ submodules skipped, npm ci ran, composer install ran, node_modules/ + vendor/ populated
--skip-bootstrap	data-machine-code	✓ no bootstrap block shown, no vendor/ in worktree
Default on PHP-only repo	data-machine-code	✓ submodules skipped, packages skipped (no lockfile), composer ran
--skip-context-injection default-bootstrap	data-machine-code	✓ context skipped, bootstrap ran

Out of scope (follow-ups)

• Repo-declared manifest (.datamachine/worktree.yml) for custom chains like nx build shared-types — option 3 in Worktree add doesn't bootstrap dependencies (node_modules, submodules) #50
• Teardown on worktree remove
• pnpm-style content-addressed node_modules sharing across worktrees

AI assistance

• AI assistance: Yes
• Tool(s): Claude Code (Opus 4.7)
• Used for: Drafted the full implementation (detector + runner + CLI wiring + smoke test + TESTING.md update). Chris challenged the initial opt-in default, which was flipped to on-by-default with a --skip-bootstrap escape hatch. Chris ran live worktree-add scenarios on data-machine and data-machine-code from the intelligence-chubes4 Studio site to confirm end-to-end behavior for both defaults and the escape hatch.