fix(extensions): harden plugin rpc bridge against stdin flush hangs and manifest request timeouts

[ZhuchkaTriplesix]

Closes #666

Summary of Changes

• Unbounded stdin flush protection: Wrapped _stdin.flush() in JsonRpcStdioClient.sendRequest with a 3-second timeout and clean request error/removal, preventing permanent UI freezes when OS pipe buffers fill up during child process hangs.
• Watchdog deadlock instant abort: When SandboxWatchdog detects a ping timeout (deadlock), PluginRpcBridge now immediately fails in-flight requests with PluginDeadlockException and disposes local handles without waiting for full RPC request timeout.
• Dynamic analytical query timeouts from manifest: Added timeout_seconds to ResourceLimits. ExtensionDriverSession now passes the manifest-configured timeout (e.g. 600s for ClickHouse) to PluginRpcBridge instead of restricting queries to the default 30s.
• Handshake timeout & stderr diagnostics: Increased default handshake timeout to 6 seconds and appended recent stderr lines from SandboxStderrPipe to the thrown PluginProtocolTimeoutException.
• Automatic dead-bridge cleanup: Added onProcessExited hook to PluginRpcBridge so ExtensionDriverSession immediately drops terminated processes from _bridges upon exit.
• Comprehensive tests: Added unit tests covering onProcessExited, handshake timeout stderr output, PluginDeadlockException, and ResourceLimits timeout parsing.