fix(bugs): fix several bugs

[ntudy]

Describe this PR

1. make sure program exit properly
2. update gitignore
3. disable fire and save hydra config
4. save result file as json with indent
5. make sure file_path is complete

Checklist for PR

Must Do

• Write a good PR title and description, i.e. feat(agent): add pdf tool via mcp, perf: make llm client async and fix(utils): load custom config via importlib etc. CI job check-pr-title enforces Angular commit message format to PR title.
• Run make precommit locally. CI job lint enforce ruff default format/lint rules on all new codes.
• Run make pytest. Check test summary (located at report.html) and coverage report (located at htmlcov/index.html) on new codes.

Nice To Have

• (Optional) Write/update tests under /tests for feat and test PR.
• (Optional) Write/update docs under /docs for docs and ci PR.

[Copilot]

Pull Request Overview

This PR fixes several bugs related to program execution, configuration management, and output formatting. The changes ensure proper exit handling, improve output readability, and update configuration settings.

• Replace Fire-based CLI with direct argument parsing for better control
• Enable Hydra logging configuration and set proper output directory structure
• Add JSON indentation for better readability and improve file path handling

Reviewed Changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 3 comments.

File	Description
apps/run-agent/main.py	Replaces Fire CLI with manual argument parsing and subprocess calls
apps/run-agent/common_benchmark.py	Adds signal handlers, switches to Hydra decorator, and fixes file path handling
libs/miroflow/src/miroflow/prebuilt/config/config.yaml	Enables Hydra logging and configures output directory
libs/miroflow/src/miroflow/logging/task_tracer.py	Adds JSON indentation for better output formatting

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[shiqian-su]

Please use !data/README.md in .gitignore to keep README file.