feat: Milestone 2 — Structured Run Manifest System (#64)

[DhanashreePetare]

Pull Request

Description

Introduces the Structured Run Manifest System (Milestone 2) for the Databus Python Client. When --manifest is passed to any of the three existing commands (download, deploy, delete), a JSON-LD manifest file is written recording the complete details of the operation — input parameters, per-file URLs, checksums, byte sizes, timestamps, success/failure status, and a structured execution summary.
The manifest uses the DataID vocabulary (the same vocabulary used by the Databus platform itself), is versioned via dbus:schemaVersion, and never writes sensitive credentials. If the manifest file already exists at the given path, it auto-suffixes (run_1.jsonld, run_2.jsonld, ...) with a warning rather than silently overwriting. Passing a directory path instead of a file path raises a clear error. Manifest writing failure warns and continues — the exit code reflects the actual operation result, not the manifest write.
The manifest is written even when the operation itself fails, capturing whatever partial results were recorded before the failure — enabling the debugging use case described in the proposal (Use Case 5).

Related Issues
#64

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• This change requires a documentation update
• Housekeeping

Checklist:

• My code follows the ruff code style of this project.
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
  • poetry run pytest - all tests passed
  • poetry run ruff check - no linting errors

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