Add CLI and API usage documentation to README

[Ulthran]

Motivation

• Provide clear, discoverable documentation for the installed CLI tools and the JSON API so users can operate the registry without inspecting source code.
• Clarify how commands interact with the configured database and document typical workflows for run/sample/annotation management.

Description

• Extended README.md with a new CLI usage section listing the installed commands (e.g. register_run, register_samples, modify_run, etc.) and showing how to use -h for help.
• Added examples showing common command-line workflows and clarified that commands use the database configured by SAMPLE_REGISTRY_DB_URI (defaulting to a local SQLite file when unset).
• Added an API usage section documenting available POST /api/* endpoints, example curl requests for register_run, modify_run, and modify_sample, and the expected JSON success/error responses.
• Clarified metadata-table payload handling for register_samples/register_annotations by specifying the sample_table JSON key or multipart/form-data file upload.

Testing

• Ran pytest -q in the environment, which failed during test collection due to a missing dependency: ModuleNotFoundError: No module named 'flask_sqlalchemy'.
• No additional automated tests were added or executed for the documentation-only change.

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Codex Task

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 70.42%. Comparing base (e0be84e) to head (403686f).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master      #66   +/-   ##
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  Coverage   70.42%   70.42%           
=======================================
  Files           9        9           
  Lines         886      886           
=======================================
  Hits          624      624           
  Misses        262      262           

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[Copilot]

Pull request overview

This PR adds comprehensive CLI and API usage documentation to the README, making it easier for users to interact with the Sample Registry without needing to inspect source code.

Changes:

• Added a CLI usage section documenting all 11 installed command-line tools with examples showing typical workflows for run/sample/annotation management
• Added an API usage section documenting the 7 available POST /api/* endpoints with example curl requests and expected JSON responses
• Fixed a minor grammar issue ("libraries utilities" → "library utilities")

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