usr/ data dir fix

[linuztx]

• Migrated user data to usr/ directory: Moved all persistent user data (chats, uploads, downloads, tasks, secrets, settings) from tmp/ to usr/ to centralize storage and simplify backups.
• Migrated .env file: Moved the root .env file to usr/.env to include environment configuration in the unified user data directory.
• Restructured Memory, Knowledge, and Instruments:
  • Moved custom knowledge and instruments to usr/knowledge and usr/instruments.
  • Consolidated memory storage into usr/memory.
  • Flattened default knowledge and instrument directories (removed default subfolder).
  • Relocated memory embeddings cache to tmp/memory/embeddings (transient data).
• Added migration script: Implemented python/helpers/migration.py to automatically move existing data from tmp/ to usr/ on startup.
• Updated system paths: Modified memory.py, persist_chat.py, task_scheduler.py, settings.py, and other helpers to reflect the new directory structure.
• Updated Frontend: Adjusted hardcoded paths in attachmentsStore.js and API documentation to point to usr/uploads instead of tmp/uploads.