[border-agent] introduce BorderAgent namespace (#12002)

This change reorganizes the `BorderAgent` related classes into a new
`MeshCoP::BorderAgent` namespace to improve code structure and clarity.

The following changes are included:

- `MeshCoP::BorderAgent` class is renamed to `Manager` and placed
  within the new `MeshCoP::BorderAgent` namespace.
- `MeshCoP::BorderAgentTracker` is renamed to `Tracker` under the
   new namespace.
- `EphemeralKeyManager` is moved from being a nested class in
  `BorderAgent` to `MeshCoP::BorderAgent::EphemeralKeyManager`.
- `EphemeralKeyManager` is now a direct member of the `Instance` class,
  simplifying accessing it.

All related calls and test files are updated to reflect these
changes.

src/core/thread/mle_ftd.cpp

@@ -2817,8 +2817,8 @@ Error Mle::SendDiscoveryResponse(const Ip6::Address &aDestination, const Discove
 #if OPENTHREAD_CONFIG_BORDER_AGENT_ENABLE
     if (Get<KeyManager>().GetSecurityPolicy().mNativeCommissioningEnabled)
     {
-        SuccessOrExit(
-            error = Tlv::Append<MeshCoP::CommissionerUdpPortTlv>(*message, Get<MeshCoP::BorderAgent>().GetUdpPort()));
+        SuccessOrExit(error = Tlv::Append<MeshCoP::CommissionerUdpPortTlv>(
+                          *message, Get<MeshCoP::BorderAgent::Manager>().GetUdpPort()));
 
         discoveryResponseTlv.SetNativeCommissioner(true);
     }