feat(cli): add update command and stop init from overwriting existing installs

[leonardobuares]

Summary

Adds lead-protocol update, a safe upgrade path for existing installations,
and closes the destructive path where re-running init replaced the whole
.agents/ tree with blank templates, wiping project-layer files
(PROJECT_RULES.md, JOURNAL.md, decisions.jsonl, ...). The new command
implements the three-layer state model the protocol already defines: the
framework layer is always refreshed, the project layer is never overwritten,
and per-pair state is never touched.

Closes #25.

Changes

• cli/src/commands/update.ts + cli/src/lib/updater.ts (new): the update
  command. Framework layer (CORE_RULES.md, PROTOCOL_RULES.md, modules/,
  schemas/, scripts/) is always refreshed to the bundled release;
  project-layer files are never overwritten, but missing project-layer seeds
  are created; .agents/local/ is never touched. Refreshes the
  <lead-protocol> blocks in CLAUDE.md / AGENTS.md and re-checks the
  .gitignore entries. Supports --yes and --dry-run, reports every file
  as updated / created / unchanged, and lists framework-dir files
  absent from the bundled release as warnings without deleting them.
• cli/src/commands/init.ts: with the protocol already installed, init now
  refuses (exit code 1) and points to update. A full reinstall stays
  available behind init --force, with an explicit warning listing the
  project-layer files that will be lost. Fresh installs are unchanged.
• cli/src/lib/scaffold.ts (new): generateGuidelines and
  ensureGitignoreEntries moved out of init.ts so both commands share them.
• cli/test/updater.test.mjs (new): 8 unit tests via native node --test
  (no new runtime dependencies) covering layer classification, overwrite,
  seed creation, project-layer skip and orphan reporting. New npm test
  script; tsup builds lib/updater.ts as its own entry so the suite
  imports the exact code that ships.
• cli/scripts/test-pack.mjs: new end-to-end scenarios against the real
  packed tarball: update --dry-run writes nothing, update --yes refreshes
  the framework layer while preserving a customized PROJECT_RULES.md and an
  orphan module, plain init refuses on an existing install, and
  init --force --yes reinstalls from scratch.
• cli/README.md: documents update and the new init behavior.
• CHANGELOG.md: [2.2.0] entry; cli/package.json bumped 2.0.3 to
  2.2.0. Numbered 2.2.0 assuming feat: add first-run setup interview gate (PROTOCOL_RULES §P10) #22 ships as 2.1.0; if feat: add first-run setup interview gate (PROTOCOL_RULES §P10) #22 does not
  land first, this can be renumbered to 2.1.0.
• @types/node added to the CLI dev dependencies: npm run typecheck
  previously failed on a clean checkout because the Node type definitions
  were never declared.

Testing

• npm run typecheck passes (after the @types/node addition).
• npm test: 8/8 unit tests pass against the built dist/lib/updater.js.
• npm run test:pack passes end to end: builds, packs the exact npm tarball,
  installs it into a throwaway consumer and exercises
  init / validate / status / update (dry-run and apply) / init guard /
  init --force.
• Manual update --dry-run against a live installation correctly reported
  all framework files unchanged and all project-layer files untouched, and
  wrote nothing.

Checklist

• Code follows project conventions
• Tests added/updated (if applicable)
• Documentation updated (if applicable)
• Protocol files follow defined schemas (.agents/ was not modified)

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