feat(core): add Manifest v2 trust boundary

[siracusa5]

Summary

Implements the first Project Profiles slice by establishing a shared Manifest v2 trust boundary before profile-aware runtime and UI work. Existing flat manifests remain behaviorally compatible and unmodified on read, while v2 selection, migration, Pack operations, settings-sync writes, source mutations, and cache isolation become deterministic and safe.

Changes

• add dependency-free Manifest v2 validation, deterministic profile selection, summaries/revisions, migration, verified backups, and ownership-safe locked atomic writes
• normalize shipped settings-sync transitional shapes into pending non-runnable sources while preserving local layers, owner metadata, mappings, and Pack assignments
• refactor Pack, engine-service source CRUD, desktop first-run creation, and desktop settings-sync writes onto the shared manifest transaction boundary
• canonicalize v2 default Pack assignments and enforce bidirectional registry/profile/layer/version invariants
• add opt-in profile/source fingerprint cache namespaces without moving existing flat-manifest caches
• add 14 manifest regression tests, Pack v2 coverage, desktop sync-derived migration coverage, and the canonical Manifest v2 reference

Test Plan

• npm test
• npm test in apps/desktop — 33 tests
• npm run build in apps/site — 28 pages plus install-page verification
• git diff --check
• Spec compliance: PR 1 slice passes
• Security review: clear
• CI checks pass

Notes

• This is implementation PR 1 of 5 from docs: define Project Profiles delivery plan #69.
• Runtime selection in resolver/MCP is PR 2; the profile-aware service API is PR 3; no profile UI is included here.
• Existing flat manifests remain unmodified on read. Agent-facing manifests should not be manually converted until the runtime-selection slice lands.