Prettify markdown RPC message rendering with proper JSON indentation

[Copilot]

RPC messages in markdown logs were using compressed single-line JSON format and showing empty payloads. This makes logs harder to read when debugging message flows.

Changes

JSON formatting (internal/logger/rpc_logger.go)

• Removed compression logic that collapsed JSON to single-line format with { ... }
• Now uses json.MarshalIndent with 2-space indentation for proper pretty printing

Empty payload handling

• Added isEffectivelyEmpty() to detect when only params: null or empty objects remain after field removal
• Modified formatJSONWithoutFields() to return isEmpty boolean alongside formatted output
• Updated formatRPCMessageMarkdown() to omit JSON code blocks when payload is effectively empty

Before:

**serena**→`tools/list`

~~~
{ "params": null }
~~~

After:

**serena**→`tools/list`

With content - Before:

**serena**→`tools/list`

~~~
{ "id": 1, "params": { "arg": "value" } }
~~~

With content - After:

**serena**→`tools/list`

~~~
{
  "id": 1,
  "params": {
    "arg": "value"
  }
}
~~~

Test updates

• Updated TestFormatJSONWithoutFields for new 3-value return signature
• Added test cases for params: null and empty object edge cases
• Added test cases verifying empty JSON blocks are not rendered

Original prompt

Prettify the markdown rendering of read and write RPC messages see below:

• 🔍 rpc serena←resp {"jsonrpc":"2.0","id":1,"result":{"tools":[{"annotations":{"destructiveHint":false,"readOnlyHint":true,"title":"List Dir"},"description":"Lists files and directories in the given directory (optionally with recursion). Returns a JSON object with the names of directories and files within the given directory.","inputSchema":{"properties":{"max_answer_chars":{"default":-1,"description":"If the output is longer than this number of characters,\nno content will be returned. -1 means the default value from the conf...

Apply JSON pretty printing.

If a JSON message only has param: null after removing field, don't show.

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