feat(update-deps): actually apply updates to package.json (default), add --dry-run

[pyramation]

Summary

makage update-deps previously only detected outdated deps and printed JSON — consumers (e.g. the constructive-hub update-constructive-deps workflow) had to reconcile with pnpm update/jq themselves. It now lives up to its name: by default it rewrites the outdated version specs in the target repo's package.json files in place.

• Prefix-preserving rewrite: ^1.0.0 → ^2.0.0, ~1.5.0 → ~1.6.0; workspace: specs untouched
• File formatting preserved (detected indentation + trailing newline)
• --dry-run (alias --check) restores the old detect-only behavior
• JSON output is a superset of before: adds updatedFiles: string[] and dry_run: boolean; MatchedDep gains file

Existing CI workflows keep working: JSON stdout schema is backward compatible, and after the tool writes specs, a pnpm install --no-frozen-lockfile syncs the lockfile (the pnpm update -r --latest / jq steps become redundant and can be dropped).

Docs (root + package READMEs, makage-overview skill) updated, plus tests for write-by-default and --dry-run.

Link to Devin session: https://app.devin.ai/sessions/a471fa4f41cc45aabc1513a2201b02f7
Requested by: @pyramation

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