feat(api): add version negotiation middleware with backward-compatible schema migration

[Darkdruce]

Closes #760

Adds withVersionMigration middleware for backward-compatible schema migration on deployment routes.

• Version negotiated via Accept-Version: application/vnd.craft.v1+json header
• v1→internal migration: flat repositoryName field maps to nested repository.name
• v2→internal: identity (v2 is the internal format)
• Unknown version returns 406 Not Acceptable
• Missing header defaults to v2 (latest) with X-Api-Deprecation-Warning response header and console warning
• Migrated body attached as req.migratedBody for downstream handlers
• X-Api-Version stamped on all responses
• Tests cover v1 migration, v2 passthrough, missing header default, 406 for unknown version, and response headers

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