Add permission checking to the remaining 7 tools that require granular
permissions:
- `edit_file`: Checks path against permission rules  
- `delete_path`: Checks path against permission rules
- `move_path`: Checks both source and destination paths
- `create_directory`: Checks path against permission rules
- `save_file`: Checks all paths, denies if any are blocked
- `fetch`: Checks URL against permission rules
- `web_search`: Checks query against permission rules

Each tool follows the pattern established in PR #46155 (terminal tool):
- `Allow` = proceed without prompting
- `Deny` = return error immediately
- `Confirm` = prompt user for confirmation

The deny > confirm > allow precedence is enforced by the
`decide_permission_from_settings()` function.

Release Notes:

- N/A

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Co-authored-by: Amp <amp@ampcode.com>