Multiple dep commands were directly accessing store without checking if
daemon was available, causing nil pointer dereferences when daemon was
running.
Fixed commands:
- dep add: Now uses RPC when daemon is available
- dep remove: Now uses RPC when daemon is available
- dep tree: Added fallback to direct storage when daemon lacks RPC support
- dep cycles: Added fallback to direct storage when daemon lacks RPC support
The commands with RPC support (add/remove) now use the daemon client
when available. Commands without RPC support (tree/cycles) fall back
to opening a direct database connection when the daemon is running.