[BUG] CLAUDE_ENV_FILE not sourced after /clear creates new session

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When /clear is executed, a new session is created and the SessionStart hook runs correctly, writing to the new $CLAUDE_ENV_FILE. However, subsequent Bash tool calls
do not have access to the environment variables from this file - they still use the environment from the original session startup.

The docs state: "Claude Code will source this file before each Bash command, making the environment persistent across all commands."

• Hook runs correctly (verified via debug logs)
• New env file is created at new path: ~/.claude/session-env/{new-session-id}/hook-0.sh
• But Bash tool calls still use environment from original session startup
• New env file is never sourced

What Should Happen?

After /clear, $CLAUDE_SESSION_ID should reflect the new session ID (e.g., bbb-222) since:

• SessionStart hook runs with source: "clear"
• Hook writes new session ID to the new $CLAUDE_ENV_FILE
• Docs say env file is sourced before each Bash command

Error Messages/Logs

Steps to Reproduce

1. Create a SessionStart hook that captures the session ID:

```json
// hooks/hooks.json
{
"hooks": {
"SessionStart": [
{
"hooks": [
{
"type": "command",
"command": "echo \"export CLAUDE_SESSION_ID='$(echo | jq -Rr 'fromjson? | .session_id // empty' <<< \"$(cat)\")''\" >> \"$CLAUDE_ENV_FILE\""
}
]
}
]
}
}

2. Start a fresh Claude Code session
  3. Run: echo $CLAUDE_SESSION_ID → outputs correct session ID (e.g., aaa-111)
  4. Run /clear command
  5. Run: echo $CLAUDE_SESSION_ID → still outputs old session ID aaa-111

### Claude Model

Opus

### Is this a regression?

I don't know

### Last Working Version

_No response_

### Claude Code Version

2.0.72

### Platform

Anthropic API

### Operating System

macOS

### Terminal/Shell

Other

### Additional Information

I am using latest version of Ghostty terminal.