Major Issues Fixed:
1. Tag Deletion Bug: Fixed critical issue where creating subtasks would delete other tags
- Root cause: writeJSON function wasn't accepting projectRoot/tag parameters
- Fixed writeJSON signature and logic to handle tagged data structure
- Added proper merging of resolved tag data back into full tagged structure
2. Persistent Migration Notice: Fixed FYI notice showing after every command
- Root cause: markMigrationForNotice was resetting migrationNoticeShown to false
- Fixed migration logic to only trigger on actual legacy->tagged migrations
- Added proper _rawTaggedData checks to prevent false migration detection
3. Data Corruption Prevention: Enhanced data integrity safeguards
- Fixed writeJSON to filter out internal properties
- Added automatic cleanup of rogue properties
- Improved hasTaggedStructure detection logic
Commands Fixed: add-subtask, remove-subtask, and all commands now preserve tags correctly
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