fix: preserve invalid configuration during automatic updates

[roodboi]

Automatic config updates could replace malformed JSON or non-object values with a new object, losing the existing settings. Updates now reject those files before writing and report the affected path with repair guidance, without echoing config contents. Read failures also refuse the update; only a genuinely missing file initializes a new config. Valid updates continue to preserve unrelated fields.

This is the bounded config-write safety prerequisite for the native configuration work. It does not add schema-version handling, change config formats, or migrate runtime state. Existing read-only fallback behavior is unchanged.

Validation: Bun 1.4.2; 37 focused config/env tests passed, including all three writer entry points, an unreadable-but-writable file, and a real CLI refusal. Full typecheck and check passed (CLI tasks executed; unchanged DB tasks reused cache). The compiled current-branch CLI independently rejected malformed config, preserved its bytes, and omitted its contents from diagnostics. Full test gate passed: CLI 2,091 passed, 68 skipped, 0 failed; unchanged DB test task reused cache (2 passed). Skips are the existing optional integration prerequisites and do not qualify native runtime behavior.

Release intent: patch correction to automatic settings persistence; no migration required.

Refs https://linear.app/hackdance/issue/HACK-1218

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[linear-code]

HACK-1218