Add constrained-runtime primary storage and explicit flush contract

[chubes4]

Problem

MDI primary mode can reconstruct WordPress from portable Markdown/JSON, but constrained and serverless runtimes currently need to reach into internal classes and rely on PHP shutdown to discover persisted changes. A Cloudflare Workers integration proved canonical Markdown cold restoration, but normal SQL interception and full bootstrap cannot yet be orchestrated through a bounded, explicit runtime contract.

Proposed contract

Add generic primary-runtime APIs that:

• bootstrap MDI in storage-only mode without CLI, recovery, migration, or abilities machinery;
• accept a caller-provided disposable SQLite index cache and identify the canonical manifest/hash it represents;
• explicitly flush pending writes without requiring process shutdown;
• return exact canonical paths created, changed, and deleted;
• support writing a canonical post/option mutation through public MDI APIs;
• keep object-store and Cloudflare concerns outside MDI.

Acceptance criteria

1. A fixture canonical root builds or hydrates a disposable SQLite index.
2. A normal WordPress post and option mutation can be explicitly flushed.
3. The flush result reports deterministic changed/deleted relative paths.
4. Destroying SQLite and reopening from the resulting Markdown/JSON reconstructs the mutation.
5. Tests prove SQLite is cache machinery and canonical files are sufficient.
6. Existing mirror and primary behavior remains compatible.

Context

This is the owning-layer primitive needed by serverless runtimes, offline editing, object-store revision systems, and agent sandboxes. Callers will stage a synchronous filesystem and replicate returned paths themselves.