PreToolUse hooks don't fire for subagents (Agent tool)

Summary

PreToolUse hooks defined in ~/.claude/settings.json fire correctly for the main agent but are silently skipped for all subagents spawned via the Agent tool. This means any hook-based command rewriting, safety checks, or instrumentation only covers a fraction of actual tool calls in multi-agent workflows.

Impact

In a Conductor environment running parallel agents, 72% of sessions are subagents. With rtk installed as a PreToolUse hook to filter/compress Bash output (saving ~40% tokens on grep, find, git, gh commands), the main agent gets the optimization but every subagent runs raw commands — wasting tokens on unfiltered output.

Measured gap (30-day window):

• Main sessions: ~11K commands went through the hook → tokens saved
• Subagent sessions: ~7K commands bypassed the hook entirely → full token cost
• Estimated waste: ~3M tokens/month from subagent commands that would have been filtered

Reproduction

1. Add a PreToolUse hook to ~/.claude/settings.json:

{
  "hooks": {
    "PreToolUse": [
      {
        "matcher": "Bash",
        "hooks": [
          {
            "type": "command",
            "command": "/path/to/my-hook.sh"
          }
        ]
      }
    ]
  }
}

1. In a session, run a Bash command directly — hook fires ✅
2. Spawn a subagent via the Agent tool that runs Bash commands — hook does NOT fire ❌

Evidence from session transcripts:

Main session transcript shows hook invocations interleaved with Bash commands:

"command":"/Users/.../.claude/hooks/rtk-rewrite.sh"
"command":"grep -rn ..."
"command":"/Users/.../.claude/hooks/rtk-rewrite.sh"
"command":"find ..."

Subagent transcript shows raw Bash commands with zero hook invocations:

"command":"grep -r ..."
"command":"find ..."
"command":"grep -n ..."

Expected behavior

All hooks (PreToolUse, PostToolUse, etc.) should propagate to subagents spawned by the Agent tool, inheriting from the same settings hierarchy (user → project → local) as the main agent.

Environment

• Claude Code version: latest (via Conductor)
• rtk version: 0.30.0
• OS: macOS (Darwin 25.5.0)
• Hook location: ~/.claude/settings.json (user-level)