Implement two-phase initialization model (discovery → registration)

[willgriffin]

Problem

Currently, class discovery and registration happen interleaved — a class can be registered at any time (decorator evaluation, manifest loading, lazy discovery during getInheritanceChain). This makes initialization order-dependent and non-deterministic.

Proposed Solution

Phase 1: Discovery

• Scan all installed SMRT packages (using discoverSmrtPackages())
• Load and parse all manifest.json files
• Build a global name → qualified-name → manifest-entry map
• Detect and report name ambiguities before any class is registered
• No mutations to ObjectRegistry.classes

Phase 2: Registration

• Compute topological order based on extends declarations
• Register all classes in dependency order (parents before children)
• After registration, compute and cache all inheritance chains
• Lock the discovery cache — no further lazy discovery permitted

Benefits

• Ambiguity detected upfront with clear error messages
• Inheritance chains guaranteed correct (parents always registered first)
• No side effects during read operations
• Deterministic regardless of import/evaluation order

Key Files

• packages/core/src/registry.ts
• packages/core/src/manifest/manifest-loader.ts
• packages/core/src/manifest/discover-smrt-packages.ts

Part of epic #1003.