refactor: reduce cognitive complexity in differential-cache (batch 3a)

[sarthakagrawal927]

Part of #117

Summary

Reduces cognitive complexity in apps/desktop/src/lib/warm-verification/differential-cache.ts by extracting helper functions from six over-complex functions, bringing every function below the cognitive complexity threshold of 20.

Changes

• prepareDependencies (CCN 24 → ≤20): Extracted #prepareDependenciesUnlocked private method from the inline #exclusive callback.
• createWritableTarget (CCN 27 → ≤20): Extracted #createWritableTargetUnlocked private method from the inline #exclusive callback.
• hashApplicationPayload (CCN 36 → ≤20): Split into collectAncestors, collectApplicationEntries, processApplicationEntry, filterApplicationDirectories, and hashApplicationRecords.
• inspectDependencyLayout (CCN 77 → ≤20): Split into walkDependencyRoot, processDependencyChild, and inspectDependencyLink.
• cleanupRoot (CCN 21 → ≤20): Extracted collectExpiredEntries and measureActiveTargets helpers.
• cleanupTransients (CCN 59 → ≤20): Split into cleanupTransientRole, processTransientEntry, handleInvalidTransient, handleStaleTransient, measureRetainedTarget, and cleanupTrash.

Verification

• pnpm exec biome lint --config-path=biome.code-health.json --only=complexity/noExcessiveCognitiveComplexity — 0 violations
• pnpm quality:complexity — PASS
• pnpm lint — PASS
• pnpm quality:duplication — PASS (0.80% < 0.81 threshold)
• All 21 differential-cache.test.ts unit tests pass

Constraints

• Pure refactoring — no behavior changes
• No suppressions (biome-ignore, eslint-disable)
• All helpers extracted to module level
• Diff: 756 insertions, 507 deletions (well under 4000/6000 line limits)