refactor(ocap-kernel): close database in Kernel.stop()

[rekmarks]

Summary

Kernel.stop() gracefully shuts down all kernel subsystems but previously did not close the database, leaving a resource leak. Since there's no realistic scenario where you'd stop the kernel but keep the database open (a restart in production means a new process with a new connection), stop() should own the full shutdown lifecycle.

• Add #kernelDatabase: KernelDatabase private field to Kernel; store it in the constructor and call .close() at the end of stop()
• Add no-op close() to the mock makeMapKernelDatabase() in ocap-kernel/test/storage.ts to satisfy the KernelDatabase type
• Remove explicit kernelDatabase.close() calls from all e2e tests — these are now handled by kernel.stop()
• Switch e2e tests that restart kernels with the same database from :memory: to temp file paths (in-memory databases are destroyed on close(), making persistence across restarts impossible)
• Refactor restartKernel and restartKernelAndReloadVat helpers to accept a dbFilename: string instead of a KernelDatabase object, opening a fresh connection internally on each call

Testing

Covered by the existing e2e test suites (system-subcluster, bip39-identity-recovery, remote-comms). The persistence tests in particular exercise the stop → close → reopen cycle that this change introduces, verifying that the database is properly closed and can be re-opened for the next kernel incarnation.

🤖 Generated with Claude Code

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Note

Medium Risk
Changes core shutdown behavior by closing the database automatically; risk is primarily around callers/tests that previously assumed the DB connection could outlive Kernel.stop() or be reused after stopping.

Overview
Kernel.stop() now closes the underlying KernelDatabase as part of shutdown, making the kernel responsible for fully releasing persistent-state resources.

To accommodate this lifecycle change, persistence/remote-comms/system-subcluster e2e tests are refactored to reopen fresh DB connections on restart (often using temp file-backed SQLite DBs) and to remove manual kernelDatabase.close() calls; remote-comms restart helpers now take a dbFilename and open the database internally each time.

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Coverage Report

Status	Category	Percentage	Covered / Total
🔵	Lines	78.22% 🟰 ±0%	6510 / 8322
🔵	Statements	78.18% ⬆️ +0.01%	6615 / 8461
🔵	Functions	76.01% 🟰 ±0%	1626 / 2139
🔵	Branches	78.16% 🟰 ±0%	2406 / 3078

File Coverage

File	Stmts	Branches	Functions	Lines	Uncovered Lines
Changed Files
packages/ocap-kernel/src/Kernel.ts	87.15% ⬆️ +0.24%	77.77% 🟰 ±0%	80.43% 🟰 ±0%	87.15% ⬆️ +0.24%	133, 281-284, 301, 325, 393-403, 495, 563, 629-632, 645, 655-656, 699, 716

Generated in workflow #3770 for commit 9bbc6e6 by the Vitest Coverage Report Action