feat(storage): complete SQLite session metadata migration

[likun666661]

Part 3 of #1370.

Depends on #1372 (and transitively #1371). This is the final stacked draft; review and merge the stack in order.

What changes

• Replaces the copied SessionHeader in new session.jsonl files with a versioned session_transcript marker containing only the session id.
• Keeps old line-1 SessionHeader files readable and importable, while refusing orphan transcript markers that have no SQLite row or deletion tombstone.
• Makes usage statistics resolve provider/model metadata from canonical sessions.sqlite, with legacy fallback only when the database does not exist.
• Adds exportLegacySessionTree() for an atomic, non-destructive downgrade/export tree with canonical headers and untouched transcript bodies.
• Adds a versioned session-metadata.json export manifest.
• Adds online SQLite backup support through backupSessionMetadataDatabase() and the store backup API, with overwrite/source-path guards.
• Exports the transcript marker and maintenance contracts from @maka/storage.

Compatibility and safety

• Existing JSONL-header sessions continue to work and are imported once.
• New marker-based sessions reopen without re-importing metadata.
• Deleted sessions remain protected by SQLite tombstones.
• Export is staged and atomically renamed; it refuses to overlap the live session tree or overwrite an existing destination.
• Backup refuses to overwrite an existing file or target the live database.

Validation

• npm test --workspace @maka/storage: 439 passed, 1 skipped
• npm run build:test: passed across all workspaces and desktop bundles
• npx biome check on all 11 changed files: passed
• git diff --check: passed
• npm run test:dist: scripts/core/storage/mcp passed; @maka/runtime retains the same 2 unrelated macOS sandbox/toolchain failures (hard-coded /usr/local executable-root expectation and Homebrew rg blocked from loading PCRE2). Runtime result: 2377 passed, 7 skipped, 2 failed.

Completes #1370 after the three-PR stack lands.

[likun666661]

DeepSeek live E2E evidence (2026-07-23)

Ran one real deepseek-chat turn with the environment-provided DEEPSEEK_API_KEY; the key was neither printed nor persisted in the repository.

• Model response: OK; stop reason: end_turn
• Usage: 178 input tokens, 1 output token; estimated cost $0.00004916
• New transcript first record: session_transcript marker with no copied metadata
• Renamed session metadata, closed/reopened the store, and verified the canonical SQLite title persisted
• Usage stats read 1 request from the marker-based session using SQLite metadata
• Exported 1 legacy-compatible session and read it back through createLegacyFileSessionStore
• Created an online SQLite backup (17 pages) and verified the restored metadata row

All live artifacts were written under a temporary /tmp workspace.