fix: Prevent StdioTransport premature disconnection (Variant 2: stream_select only)

[ArtemYurov]

Problem:

• MCP server disconnects after ~60 seconds of inactivity
• fread() blocks and returns false when no data available
• This triggers "Failed to read from STDIN" error and breaks the listening loop

Solution (Variant 2):

• Use stream_select() with 1-second timeout to check data availability before reading
• Remove feof() check, rely entirely on stream_select() and $this->closing flag
• Enable graceful shutdown by checking $this->closing flag every second
• Prevents blocking while maintaining responsive shutdown

Testing:
✅ Tested for 150+ seconds without disconnections
✅ Compatible with macOS and other UNIX systems
✅ Graceful shutdown works correctly

Changes:

• Added stream_select() before fread() to wait for available data
• Replaced while (!\feof($this->input)) with while (!$this->closing)
• Short 1-second timeout allows periodic check of $this->closing flag
• Fixed $deferred->resolve() to pass null argument (line 144)

Comparison to Variant 1:

• Simpler code without feof() check
• Relies entirely on stream_select() for EOF detection
• May have edge cases on systems where stream_select() doesn't detect EOF properly