[shoom1]

A warning logged during a turn (here arxiv_rate_limited) was written straight to stderr. thinking-prompt doesn't capture stderr, so the line landed on the prompt line and left the screen garbled. Any of the framework's ~100 logger.warning calls could do this at the default log level.

What changes

• Every logger writes to one stream, agentic_cli.logging.LOG_STREAM: structlog's PrintLoggerFactory and the standard library's StreamHandler. With no sink it writes to sys.stderr as before. log_lines_to(sink) sends each complete line to a sink instead, keeping each thread's partial line separate.
• While the prompt runs, BaseCLIApp sets a sink, _log_lines_above_prompt. It hands each line to the event loop with call_soon_threadsafe, and the loop adds it to the session with add_rich, so it prints above the prompt. This works whichever thread logged it, including an executor thread with no access to the loop's context.
• The warnings hook writes Python's other warnings to the same stream.
• The format and the level are unchanged. When the prompt ends, lines go to stderr again.

Tests

• A pty test runs the console app with its stderr sent to a file. A turn logs from the loop, from asyncio.to_thread, and from a plain thread, logs a standard-library warning, and raises a Python warning. On the old code all four lines went to the file (RED); now all four reach the screen and none reach the file.
• A unit test checks that lines from any thread reach the session on the loop thread, and that stderr is used again afterwards. Mutation check: adding the line on the calling thread fails the test.
• tests/conftest.py::logging_configured puts structlog's configuration back after a test, including its processors list. Without it, a second configure_logging() left capture_logs() tests later in the run capturing nothing.
• Full offline suite: 6069 passed, plus the known empty-HOME artifact test_workspace_path_expansion.