usr/ data dir

[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.
• Restructured Memory, Knowledge, and Instruments:
  • Moved custom knowledge and instruments to /usr/knowledge/custom and /usr/instruments/custom.
  • 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.
• Cleanup: Removed individual ignores in .gitignore in favor of a single /usr exclusion rule