fix: resolve issues #135-#146 and harden tools/core

[minorcell]

Goal

Apply and validate all fixes requested in issues #135 through #146.

Summary

• Security and protocol hardening:
  • Remove data: support from webfetch (fix: Remove data: protocol from webfetch tool to prevent security risks #135)
  • Harden shell argv quoting semantics (fix: Review shellJoin regex for potentially dangerous characters #138)
  • Block apply_patch symlink escape via realpath checks (fix: Prevent apply_patch sandbox escape via symlink targets #143)
• Core/runtime correctness:
  • Clarify accumulateUsage total computation expression (fix: Correct operator precedence in accumulateUsage function #136)
  • Add JsonlHistorySink.close() + serialized write queue; wire close path in session runtime (fix: Add close method and fix race condition in JsonlHistorySink #137)
  • Structured stderr logging in emitEventToSinks failure path (fix: Replace console.error with structured logging in emitEventToSinks #140)
  • Circular reference and depth handling in stableStringify (fix: Add circular reference handling to stableStringify function #142)
• Tool orchestration/runtime robustness:
  • Input size/object-shape guardrails in parseToolInput (fix: Add size limits and improve type safety in parseToolInput #139)
  • Preserve unread output across max_output_tokens truncation boundaries (fix: Preserve unread exec output when max_output_tokens truncates a chunk #144)
  • Make timeout_ms enforce execution deadline for shell wrappers (fix: Enforce timeout_ms in shell and shell_command to prevent orphan processes #145)
  • Enforce active exec session cap (MAX_SESSIONS) (fix: Enforce active session cap in UnifiedExecManager #146)
• Follow-up tracking:
  • Recorded behavior/compatibility deltas in docs: 记录 #135-#146 修复带来的行为变更与兼容性影响 #148.

Validation

• pnpm run test:core
• pnpm run test:tools

Both suites pass locally.