Gate initial graph seeding behind --seed

[PabloZaiden]

Summary

• Added CLI parsing for a --seed flag and wired startup seeding through it.
• Prevented initial graph bootstrap unless storage is empty and --seed is explicitly provided.
• Deferred JSON storage directory creation until data is actually saved.
• Updated README and tests to cover seeding behavior, CLI handling, HTTP/app startup, and storage directory creation.

Tests

• Added coverage in src/server/app.test.ts, src/server/cli.test.ts, and src/storage/json.test.ts.

[Copilot]

Pull request overview

This PR changes Link’s startup behavior so the JSON graph is no longer bootstrapped automatically on first run. Instead, seeding default node/edge types is now an explicit CLI-driven action, while the storage layer stays read-only until data is actually written.

Changes:

• Added --seed CLI parsing and threaded the flag through app startup.
• Changed JsonGraphRepository so bootstrap seeding only happens when explicitly requested on an empty graph, and directory creation is deferred until writes.
• Updated tests and README to reflect explicit seeding, read-only startup, and lazy storage directory creation.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/storage/json.ts	Reworked repository initialization to make seeding explicit and defer directory creation until writes.
src/storage/json.test.ts	Added repository tests for read-only startup, explicit seeding, lazy directory creation, and empty-graph behavior.
src/server/cli.ts	Added CLI option parsing for --validate and --seed.
src/server/cli.test.ts	Added unit coverage for CLI flag parsing combinations.
src/server/app.ts	Threaded seed options into app/repository startup and added a startApp options object.
src/server/app.test.ts	Added tests covering normal startup vs explicit seeded startup.
src/index.ts	Switched entrypoint startup/validation flow to use parsed CLI options.
src/api/http.test.ts	Updated integration tests to seed repositories explicitly before CRUD/API assertions.
README.md	Documented explicit seeding, lazy directory creation, and updated usage examples.
Dockerfile	Removed eager /data directory creation from the runtime image.

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