Add copy-on-write syncDirs bootstrap

[sjquant]

Why

New worktrees should become usable quickly while keeping dependency and build state correct for the new checkout. A CoW seed is only an optimization; the detected tool still performs authoritative repair after synced local files are available.

Changes

• Keep syncDirs as an advanced, generic relative-directory CoW feature with APFS clonefile or mandatory Linux reflinks, never ordinary-copy fallback or package-manager behavior.
• Resolve dependencyBootstrap across global, per-repo global, and local config with explicit values taking precedence over prompting.
• Add an interactive tool-aware policy prompt for gji new and gji pr: reuse and repair, install fresh, or skip. Persist the choice through the existing local/global installSaveTarget behavior; JSON, headless, and dry-run modes never prompt and retain off when unset.
• Detect PR bootstrap adapters from the actual PR worktree while selecting only safe project-local seed sources.
• Support pnpm, Yarn, npm, uv, Cargo, and project-local Ruby/Bundler bootstrap targets with deterministic repair commands. npm remains install-only; Bundler is restricted to vendor/bundle and receives an explicit local bundle path.
• Preserve the lifecycle CoW seed → syncFiles → dependency/build repair or install → after-create, and stop setup before repair, prompts, or hooks when syncFiles fails.
• Preserve pnpm metadata regeneration, runtime compatibility checks, symlink and destination safety, clone reservations and locks, cached unsupported-CoW failures, partial-clone cleanup, no-overwrite publication, and protection of pre-existing targets.
• Keep after-create as the project-specific escape hatch for generation, local services, and environment commands.
• Keep human and JSON output paths separate, and report sync-file failures independently from dependency bootstrap failures.
• Update README, website docs, and black-box coverage for policy persistence, explicit precedence, non-interactive behavior, Bundler, lifecycle ordering, fallback, cleanup, output states, and failure paths.

Validation: pnpm test (39 files, 692 tests), pnpm typecheck, pnpm build, pnpm docs:build, pnpm generate-man, and Biome checks all pass.