Add Primitive repository APIs (`ResourceRepository`, `ToolsRepository`, ... )

[sdelamo]

Currently, McpStatelessAsyncServer and McpAsyncServer save resources, tools, prompts, and completionswithCopyOnWriteArrayList`.

https://github.com/modelcontextprotocol/java-sdk/blob/main/mcp-core/src/main/java/io/modelcontextprotocol/server/McpStatelessAsyncServer.java#L60-L68

I want to provide an API (for example, ResourcesRepository) that, by default, uses the current in-memory strategy but can be replaced, for example, by a dynamic implementation that returns a different list of resources depending on the currently authenticated user.

[chemicL]

I believe the repository-oriented design should be able to address the needs expressed in #593 (comment). If we can unify these ideas in this issue we could close #593 and make progress designing a comprehensive solution with this issue. @tzolov, @sdelamo WDYT?