Fix AI tool prompt alignment and diagnostics

[codedogQBY]

Summary

• keep AI system workflow instructions aligned with the tools actually registered for the turn
• add per-tool timeout defaults and concise tool start/end/timeout diagnostics
• make tool schemas tolerate common JSON object/array and numeric-string arguments
• make early tool-call UI dedupe match by tool name instead of a raw counter

Verification

• corepack pnpm --filter @readany/core exec tsc --noEmit
• corepack pnpm --filter @readany/core exec vitest run src/ai/tests/system-prompt.test.ts src/ai/tests/reading-agent-tools.test.ts src/ai/tests/tool-call-state.test.ts src/ai/tests/tool-result.test.ts