Add persistent store implementation (replace in-memory store)

[JAORMX]

Summary

Waggle currently uses an in-memory MemoryStore (pkg/infra/store/memory.go) that implements the environment.Repository interface. All environment state is lost on restart. We need a persistent store so environments can survive server restarts and support operational use cases like auditing.

Current Architecture (DDD)

The codebase follows Domain-Driven Design with clean separation:

• Domain interface: pkg/domain/environment/repository.go defines Repository with 5 methods: Save, FindByID, FindAll, Delete, Count
• Current adapter: pkg/infra/store/memory.go implements Repository with a map[string]*Environment + sync.RWMutex
• Service layer: pkg/service/environment.go depends on the Repository interface (not the concrete store)
• Wiring: cmd/waggle/main.go:59 instantiates store.NewMemoryStore() and injects it

The service layer calls Save() after every state transition (Creating, Running, Error, Destroying) and Delete() on destroy. FindByID() and FindAll() are read-only. All methods accept context.Context.

Critical contract: copy semantics

The MemoryStore returns copies on both Save() and FindByID() to prevent aliasing bugs. The persistent store must maintain equivalent isolation — a mutated *Environment returned from FindByID() must not affect the stored state until Save() is called again.

Approach

New adapter in pkg/infra/store/

Add a new file (e.g., bolt.go or sqlite.go) implementing environment.Repository. The implementation choice depends on requirements:

Option	Pros	Cons
bbolt (embedded KV)	Zero config, single file, no external deps	No SQL, limited query flexibility
SQLite (embedded SQL)	SQL queries, mature, well-understood	CGO dependency (unless modernc)

For a single-binary MCP server, bbolt or modernc SQLite (pure Go) are good fits — no external database to manage.

Serialization

The Environment struct needs to be serialized/deserialized. Options:

• JSON (simple, human-readable, already used in MCP responses)
• Protobuf (compact, schema-versioned — overkill for now)

Wiring change

Only cmd/waggle/main.go needs to change:

// Before
repo := store.NewMemoryStore()

// After (example with bbolt)
repo, err := store.NewBoltStore(cfg.DataDir + "/waggle.db")
if err != nil {
    return fmt.Errorf("open store: %w", err)
}
defer repo.Close()

Configuration

Add a WAGGLE_STORE_PATH env var (or reuse DataDir) for the database file path. The MemoryStore should remain available for testing and as a fallback.

Acceptance Criteria

• New Repository implementation in pkg/infra/store/ with persistent storage
• Implements all 5 methods: Save, FindByID, FindAll, Delete, Count
• Returns environment.ErrNotFound for missing entities (matching MemoryStore contract)
• Copy semantics maintained (returned *Environment is independent of stored state)
• Context respected for cancellation/timeout on all operations
• MemoryStore kept for tests (not deleted)
• Wiring in main.go updated to use persistent store by default
• Configuration via environment variable for store path
• Table-driven parallel unit tests matching memory_test.go coverage
• doc.go with SPDX headers if new package created