Ask command is not saved in the defined JSON file during non interactive mode.

[fklement]

Problem:

When using the --non-interactive mode with --output-file and use the ask command to query a question, the output is printed and not written to the defined JSON file.

Example command:

> uv run metis --codebase-path /codebase/application --non-interactive --output-file "./results/asked_question.json" --command "ask Whats the repo name?" --chroma-dir ./chromadb_application
⠧ Thinking...
Metis Answer:

Code Context: The repository name is not provided in the context information.

Documentation Context: The repository name is "application".

Expected behaviour:

When defining an output file in non-interactive mode, I assume that the output will be saved in the .json file.