Add opt-in monorepo initializer

[chailandau]

Category: new-feature
User Impact: Monorepo users can safely bootstrap root and child Ghost packages without manually discovering every workspace path.
Problem: Ghost already supports root-to-child fingerprint stacks, but initialization required users to know each child path and run ghost init --scope ... by hand.
Solution: Add an opt-in ghost init --monorepo mode that creates or preserves the root package, detects workspace child package roots from deterministic metadata, and prints scoped init commands by default. Add --apply for explicit child package creation, keeping plain ghost init unchanged.

Validation:

• pnpm test: passed, 390 tests
• pnpm check: passed
• pnpm build: passed in pre-push hook

Changeset: added minor changeset for the new public CLI flag/capability.

Ghost Review:

• node packages/ghost/dist/bin.js check --base origin/main --format json: passed
• node packages/ghost/dist/bin.js review --base origin/main --include-memory --format json: ran successfully

File changes

.changeset/green-monorepos-init.md
Adds the minor release note for the new monorepo initializer.

README.md
Documents the safe ghost init --monorepo plan mode and explicit --apply mode.

apps/docs/src/content/docs/cli-reference.mdx
Adds the monorepo initialization commands and behavior to the CLI reference.

apps/docs/src/generated/cli-manifest.json
Regenerates CLI metadata so docs expose --monorepo and --apply.

docs/fingerprint-format.md
Documents the monorepo initializer alongside nested package stack behavior.

docs/superpowers/plans/2026-06-22-monorepo-initializer.md
Captures the implementation plan and execution checklist used for the change.

docs/superpowers/specs/2026-06-22-monorepo-initializer-design.md
Captures the approved design and risk decision for plan-by-default behavior.

packages/ghost/src/fingerprint-commands.ts
Extracts init registration into a focused command module and keeps the broader fingerprint command registry under the file-size guard.

packages/ghost/src/init-command.ts
Registers ghost init, including existing root/scope behavior plus the new monorepo options and validation.

packages/ghost/src/monorepo-init-command.ts
Implements plan/apply output, root creation or preservation, child skip/create handling, and scoped command formatting.

packages/ghost/src/scan/index.ts
Exports the monorepo candidate detector for CLI use.

packages/ghost/src/scan/monorepo-init.ts
Adds deterministic workspace metadata detection for package.json workspaces and pnpm workspaces.

packages/ghost/test/cli.test.ts
Adds coverage for plan mode, apply mode, skipped existing packages, custom --memory-dir, GHOST_MEMORY_DIR, pnpm workspaces, and invalid option combinations.

Screenshots/Demos: N/A