[BUG] Environment Variables from SessionStart Hooks are not cleared on /clear

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?

I have a SessionStart Hook which sets a SESSION_ID environment variable so it can be used to create and find state files in .claude/planning/{$SESSION_ID}

After running /clear the SessionStart Hook is run again and correctly sets the new SESSION_ID in the passed CLAUDE_ENV_FILE but claude-code continues to use the SESSION_ID environment variable from the previous session

What Should Happen?

After running /clear the environment variables from the previous session should be gone.
Or at the very least the SESSION_ID from the newly run hook should replace the old one.

Error Messages/Logs

❯ please run `echo $SESSION_ID_PROJECT`                                                        
                                       
● Bash(echo $SESSION_ID_PROJECT)                                                               
  ⎿  425df70f-01ea-4c34-bf27-800a41367a21 

❯ /clear                                                                                       
  ⎿  (no content)

❯ please run `echo $SESSION_ID_PROJECT`                                                        

● Bash(echo $SESSION_ID_PROJECT)
  ⎿  425df70f-01ea-4c34-bf27-800a41367a21

● The value is 425df70f-01ea-4c34-bf27-800a41367a21.

  This appears to be from a previous session - the system-reminder shows the new session ID
  should be 791755fa-b4c3-45dc-a4d8-a931403fb4ff. This confirms the /clear command isn't
  properly clearing/resetting environment variables.

Steps to Reproduce

I created https://github.com/vonAffenfels/claude-code-clean-does-not-clear-env to show the behaviour.

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.76 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

IntelliJ IDEA terminal

Additional Information

_No response_