Implement Phase 2 items and Phase 3 task 14 & task 17 from plan.md

[RafsanNeloy]

Contributor checklist

• This pull request is on a separate branch and not the main branch
• I ran pre-commit run --all-files and/or pytest as appropriate (see Tests in the README). A clean Ruff/pre-commit run is necessary but not sufficient—behavior still needs tests and review.
• If CLI output changed intentionally, I updated capture_tests/expected_captures.txt
• If command behavior changed, I checked normal, --json, and --jsonl output modes (or noted why not applicable)
• Data-layer modules do not add direct print() calls for user-visible output
• Public command names, flags, and default behavior remain compatible unless this PR explicitly documents a breaking change
• No credentials, tokens, or session data appear in code, fixtures, logs, or this PR description

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Type of change

• Bug fix
• New feature or command behavior
• Documentation
• Tests only
• Other (describe below)

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Description

Implemented improved API request handling by adding a default HTTP timeout, strengthening connection and timeout error handling with clearer user feedback, and extending JSON output support across multiple commands. also implemented confirmation prompts for destructive commands and version handling.

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Related issue

• Closes Phase 2 Progress Tracker #47

[dlq]

Thanks, Rafsan! This looks close: pre-commit and unit tests are passing, but the capture test is failing because the expected CLI capture was not updated for an intentional JSONL output change.

The failing command is:

cbrain --jsonl tag create --name NewTag3 --user-id 2 --group-id 3

It now outputs JSONL like this:

{"id":102,"name":"NewTag3","user_id":2,"group_id":3}

but capture_tests/expected_captures.txt still expects:

Tag created successfully!

Could you update capture_tests/expected_captures.txt for this changed --jsonl output and rerun the capture tests? Once that passes, this should be much closer to ready.

[RafsanNeloy]

Thanks, Rafsan! This looks close: pre-commit and unit tests are passing, but the capture test is failing because the expected CLI capture was not updated for an intentional JSONL output change.

The failing command is:

cbrain --jsonl tag create --name NewTag3 --user-id 2 --group-id 3

It now outputs JSONL like this:

{"id":102,"name":"NewTag3","user_id":2,"group_id":3}

but capture_tests/expected_captures.txt still expects:

Tag created successfully!

Could you update capture_tests/expected_captures.txt for this changed --jsonl output and rerun the capture tests? Once that passes, this should be much closer to ready.

Yes, I'll update it. I've marked it as a draft PR for the remaining works. After that it will be ready for review asap.

[dlq]

Looks good!