Complete git notes preservation documentation and cleanup

- Added comprehensive documentation for notes preservation during rebasing/squashing
- Updated CLAUDE.md with backup/restore command examples
- Documented best practices for preserving conversation context during destructive git operations
- Cleaned up test files

All git notes preservation features are now complete and documented.

CLAUDE.md

@@ -58,6 +58,7 @@ This is a Claude Code hooks system that intercepts and processes all tool usage
 **`cmd/`** - CLI interface using Cobra
 - `run.go` - Handles hook execution (called by Claude Code)
 - `install.go` - Manages hook installation/uninstallation
+- `notes.go` - Git notes backup, restore, and management commands
 
 ### Type Safety and JSON Handling
 
@@ -138,6 +139,20 @@ git log --show-notes=claude-conversations --oneline
 - Commit context (command and git output)
 - Claude version information
 
+**Notes Preservation**:
+```bash
+# Backup all conversation notes
+./hooks notes backup [filename]
+
+# List all commits with notes
+./hooks notes list  
+
+# Restore from backup after destructive operations
+./hooks notes restore <filename>
+```
+
+The system automatically warns before destructive git operations and configures git to preserve notes during rewrites.
+
 ## Key Design Principles
 
 - **No Type Casting**: All JSON handling uses proper unmarshaling to typed structs

README.md

@@ -223,6 +223,47 @@ git fetch origin refs/notes/claude-conversations:refs/notes/claude-conversations
 git config remote.origin.fetch '+refs/notes/*:refs/notes/*'
 ```
 
+### Preserving Notes During Rebasing and Squashing
+
+**⚠️ Important**: Git notes can be lost during rebase, squash, and other destructive operations. This hooks system includes comprehensive protection:
+
+#### Automatic Protection
+
+The system automatically:
+- **Warns before destructive operations** like `git rebase`, `git reset --hard`, `git commit --amend`
+- **Configures git to preserve notes** during rebase operations
+- **Provides backup and restore commands** for manual recovery
+
+#### Manual Backup and Restore
+
+```bash
+# Backup all conversation notes
+./hooks notes backup my-notes-backup.json
+
+# List all commits with notes
+./hooks notes list
+
+# Restore notes from backup (after rebase/squash)
+./hooks notes restore my-notes-backup.json
+```
+
+#### Automatic Git Configuration
+
+The system configures git to preserve notes:
+```bash
+git config notes.rewrite.mode copy
+git config notes.rewriteRef refs/notes/claude-conversations
+```
+
+This ensures notes are automatically copied to new commit hashes during rebasing.
+
+#### Best Practices
+
+1. **Before major rebasing**: Run `./hooks notes backup` to create a safety backup
+2. **Use the copy mode**: The system auto-configures git to copy notes during rewrites
+3. **Check after operations**: Run `./hooks notes list` to verify notes are preserved
+4. **Manual restore**: Use `./hooks notes restore` if any notes are lost
+
 ## Testing Hooks
 
 Test individual hooks by piping JSON:

rebase_test.txt

@@ -1,2 +0,0 @@
-# Test rebase notes preservation
-# Test commit 2