storage(doctor): preserve journal mode during diagnosis

[TusanHomichi]

doctor previously set WAL through the writable backup options before checking journal mode. A DELETE-mode installation now stays byte-identical and reports expected wal, got delete.

• Add an explicitly read-only diagnostic connection with creation disabled and no journal-mode setter; preserve writable startup and backup options.
• Share invariant verification on one acquired connection and label connection-local PRAGMAs honestly.
• Add seven integration tests covering missing databases, rejected writes, DELETE-mode preservation, stopped WAL, live WAL-only commits, and separate-process Unix permission cases.
• Record ADR 0016: SQLite may create WAL sidecars or update shared-memory coordination. Read-only storage without usable sidecars fails diagnosis; no immutable or unlocked fallback. Update operator documentation, retaining the warning for older deployed preview binaries.

Validation at 94fd4f3: web install/check/build, Rust fmt/Clippy, all 125 Rust tests, explicit debug binary build, all eight browser tests (npm run e2e -- --trace on), and the original #56 CLI reproduction pass. npm audit --json still exits 1 for the three low-severity entries already tracked in #54.

The first browser run overlapped the Rust suite and finished 7/8: the draft workflow exhausted its overall 60-second timeout at drafts.spec.ts:394 during login. After inspecting the timeout and pending-login snapshot, the browser suite ran separately in the documented sequence with tracing: all eight passed in 41.9 seconds, including the draft workflow in 38.9 seconds. Other workflows also improved from 13–22 seconds to 11–12 seconds, supporting resource contention as the cause. No test timeout or application behavior changed.

The filesystem tests use Unix permissions with an unprivileged runner; they are not a mounted read-only filesystem or crash-recovery drill. The preview has not been deployed.

Closes #56.

[chatgpt-codex-connector]

Codex Review Summary

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-04T23:53:03.897836Z	94fd4f3	Draft marked ready

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