feat: sync agent-created MCP workspaces into the GUI

[anbturki]

The app displayed only user-added roots and ignored the MCP server's workspace registry (~/.docsreader/workspaces.json), so workspaces an agent created (e.g. the default ~/notes, or project-scoped folders) were invisible until added by hand - the app looked empty even though agents had written docs.

What changed

• New Tauri commands list_registry_workspaces and registry_dir over the existing docsreader-core registry loader; a core existing_workspaces filter drops entries whose directory no longer exists so a deleted workspace never shows as a broken empty root.
• useLibrary sync: merges registry workspaces into the sidebar on launch, live-watches the registry directory (plus a window-focus fallback) so agent-created workspaces appear without a restart, selects the first when the app was empty, and remembers dismissals so a removed workspace stays gone.
• Concurrency hardening: an authoritative roots ref and serialized store writes prevent concurrent reconcile/add/remove from dropping an entry; dismissals are recorded only for actual registry workspaces, not manually added folders.

Tests

• Rust: existing_workspaces filter; registry loader present/absent/malformed.
• Frontend: reconcile adds to an empty app and selects the first, keeps stored roots, skips dismissed, does not steal an existing active root, records a dismissal only for synced workspaces.

Full suite green: 98 Rust tests, 43 frontend tests, clippy -D warnings, tsc clean.