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