Implement Phase 2 items and Phase 3 task 14 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.

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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.