feat(cli): auto-generate STUDY.json metadata for init and run outputs

[GaneshPatil7517]

This PR adds automatic STUDY.json generation for studies created via concore init and workflow outputs generated via concore run.
The goal is to improve study traceability with lightweight, machine-readable metadata.

What Changed

1. Added a metadata writer that creates STUDY.json with:

• generated_by
• concore_version
• timestamp
• python_version
• platform
• study_name
• working_directory
• tools_detected
• checksums
• schema_version

2.Integrated metadata generation into:

• concore init
• concore run

3.Extended CLI tests to verify:

• STUDY.json is created
• expected keys and values are present for init and run flows

4. Updated openJupyter security tests to run reliably in test mode by setting required test environment variables, including FLASK_SECRET_KEY.

Why

• Improves reproducibility metadata for generated studies.
• Provides clear provenance for how and where artifacts were generated.
• Keeps the change additive and non-breaking.

Validation
Local test results:

• 160 passed
• 0 skipped
• 0 failed

Compatibility

• No breaking changes to existing commands or workflows.
• Metadata file is additive and optional for downstream usage.

Fixes #502

[Copilot]

Pull request overview

This PR adds automatic generation of a STUDY.json metadata file to improve traceability for studies created via concore init and workflow outputs generated via concore run.

Changes:

• Added a write_study_metadata(...) helper to generate STUDY.json with provenance, tool detection, and checksums.
• Integrated metadata generation into concore init and concore run flows.
• Extended CLI and openJupyter security tests to validate metadata creation and ensure required env vars (e.g., FLASK_SECRET_KEY) are set in test mode.

Reviewed changes

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

Show a summary per file

File	Description
concore_cli/commands/metadata.py	Introduces the STUDY.json writer (checksums/tool detection/provenance fields).
concore_cli/commands/init.py	Calls metadata writer during project initialization and prints metadata info.
concore_cli/commands/run.py	Calls metadata writer after workflow generation and prints metadata path.
tests/test_cli.py	Adds assertions that STUDY.json is created with expected fields for init/run.
tests/test_openjupyter_security.py	Patches required env vars (incl. FLASK_SECRET_KEY) to make security tests reliable.

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[GaneshPatil7517]

hello @pradeeban the pr is ready to review please review it when you are free....