Change client session identification for project activation

Owing to the session identification issues described in this comment, we should change the handling of client sessions for Serena v2, fully moving session identifier handling into Serena instead of relying on the MCP - which was never entirely reliable to begin with (depended on the client).

• We can handle it as in the serena_repl tool, requiring the client to pass the session identifier obtained via initial_instructions.
• Subsequently, we can remove the session_id magic in Tool.