Change bitfields from enum to uint64 (#125)

Resolves #121

In some languages enum fields are strongly typed and it is impossible
to assigned OR-ed values to the enum field. This makes impossible to
compose the bit fields properly.

This changes all bit field declarations from enum to uint64. The enum
declarations stay, so that bit definitions are clear.

specification.md

@@ -401,13 +401,13 @@ message AgentToServer {
     string instance_uid = 1;
     uint64 sequence_num = 2;
     AgentDescription agent_description = 3;
-    AgentCapabilities capabilities = 4;
+    uint64 capabilities = 4;
     AgentHealth health = 5;
     EffectiveConfig effective_config = 6;
     RemoteConfigStatus remote_config_status = 7;
     PackageStatuses package_statuses = 8;
     AgentDisconnect agent_disconnect = 9;
-    AgentToServerFlags flags = 10;
+    uint64 flags = 10;
 }
 ```
 
@@ -586,8 +586,8 @@ message ServerToAgent {
     AgentRemoteConfig remote_config = 3;
     ConnectionSettingsOffers connection_settings = 4;
     PackagesAvailable packages_available = 5;
-    Flags flags = 6;
-    ServerCapabilities capabilities = 7;
+    uint64 flags = 6;
+    uint64 capabilities = 7;
     AgentIdentification agent_identification = 8;
     ServerToAgentCommand command = 9;
 }
@@ -630,7 +630,7 @@ This field is set when the Server has packages to offer to the Agent. See
 
 #### ServerToAgent.flags
 
-Bit flags as defined by Flags bit masks.
+Bit flags as defined by ServerToAgentFlags bit masks.
 
 `Report*` flags can be used by the Server if the Agent did not include the
 particular portion of the data in the last AgentToServer message (which is an allowed