Resume from stale batches

[adammcdonagh]

This pull request introduces a new environment variable to control batch resume behavior, updates documentation to reflect this change, and bumps several dependencies to their latest versions. It also includes some improvements to pre-commit configuration and development tooling. The most significant changes are the addition of OTF_STALE_RUNNING_LOG_SECONDS for safer batch resumption, dependency upgrades, and improved documentation for developers and automated agents.

Batch resume improvements:

• Added support for the OTF_STALE_RUNNING_LOG_SECONDS environment variable, allowing batch jobs to resume from a _running log file if it has been inactive for a specified number of seconds. This helps prevent resuming from logs still in use by active batches. The logic was added to get_latest_log_file in src/opentaskpy/otflogging.py and is covered in the documentation. [1] [2]
• Updated test fixture cleanup in tests/fixtures/ssh_clients.py to handle the new environment variable.

Documentation and onboarding:

• Added a comprehensive AGENTS.md file to help autonomous agents and maintainers understand the architecture, contracts, and best practices of the Open Task Framework.
• Updated README.md to document the new OTF_STALE_RUNNING_LOG_SECONDS variable and clarified batch resume behavior. [1] [2]
• Updated CHANGELOG.md to reflect the new feature and dependency changes.

Dependency and toolchain updates:

• Bumped minimum versions for key dependencies in pyproject.toml: jsonpath-ng, jsonschema, paramiko, requests, referencing, tenacity, and python-gnupg.
• Upgraded development dependencies: black to 26.3.1 and pylint to 4.0.
• Updated .pre-commit-config.yaml to use black 26.3.1 and improved codespell configuration to exclude pgp.py. [1] [2]

Miscellaneous:

• Removed obsolete Ruff ignore for UP038 in pyproject.toml.
• Updated GPG keys used for encryption testing

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.02%. Comparing base (cd398aa) to head (3fe58a9).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #155      +/-   ##
==========================================
+ Coverage   88.99%   89.02%   +0.03%     
==========================================
  Files          22       22              
  Lines        2698     2706       +8     
==========================================
+ Hits         2401     2409       +8     
  Misses        297      297              

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