feat(v3): migrate workspace to API, Tauri desktop, and v3 crates; remove legacy MCP stack

- Add apps/api, desktop Tauri shell, domain/application/crypto/device-auth/infrastructure-db
- Replace desktop-daemon vault integration; drop secrets-core and secrets-mcp*
- Ignore apps/desktop/dist and generated Tauri icons; document icon/dist steps in AGENTS.md
- Apply rustfmt; fix clippy (collapsible_if, HTTP method as str)

apps/desktop/README.md

@@ -0,0 +1,6 @@
+# apps/desktop
+
+This directory is reserved for the v3 Tauri desktop shell.
+
+The desktop UI is intentionally kept separate from `crates/desktop-daemon` so
+that closing the main window does not terminate the local MCP process.