[BUG] Session resume pollutes conversation files with duplicate system messages, hiding conversation history

Bug Description

When using claude --continue or claude --resume to restore a previous conversation, the conversation content appears to be missing/invisible.

After investigation, I found that the conversation JSONL files are being polluted with excessive duplicate mode and permission-mode system messages every time a session is resumed.

Environment

• OS: Windows 11 Home China (10.0.26200)
• Claude Code Version: 2.1.173
• Shell: PowerShell 5.1

Steps to Reproduce

1. Start a conversation with claude
2. Have a conversation with multiple messages
3. Exit the session
4. Resume with claude --continue
5. Repeat steps 2-4 multiple times
6. Notice that previous conversation content becomes invisible

Root Cause

Each time claude --continue is used, new mode and permission-mode system messages are appended to the conversation JSONL file without deduplication.

Example from my conversation file (038b0285-e2f9-4e6f-9b36-12b8bca4af4f.jsonl):

| Metric | Before Cleanup | After Cleanup |
|--------|----------------|---------------|
| Total lines | 147 | 71 |
| System messages | 78 (39 mode + 39 permission-mode) | 2 (1 mode + 1 permission-mode) |
| Actual messages | 13 (6 user + 7 assistant) | 13 |
| Ratio (system:actual) | 6:1 | 0.15:1 |

Impact

• Conversation files grow unnecessarily large
• When loading conversation, system messages consume the context window
• Actual conversation content is pushed out and becomes invisible
• Users think their conversation history has been lost

Suggested Fix

1. Deduplicate system messages - Only keep the latest mode and permission-mode message when resuming a session
2. Or compress system messages - Store only the current state rather than appending duplicate state changes
3. Or add cleanup logic - When loading a conversation, automatically remove duplicate system messages

Workaround

I wrote a PowerShell script to clean up the duplicate messages:

1. Read each JSONL file
2. Keep only the first occurrence of each unique mode/permission-mode value
3. Write the cleaned content back

This reduced my conversation files by ~50% and restored visibility of conversation history.

Additional Context

• 63 conversation files were affected in my ~/.claude/projects/ directory
• Total of 1287 duplicate system messages removed
• The issue is more severe for shorter conversations that have been resumed many times