refactor: first step to outsource query command (#339)

This is an attempt to fulfil the request outlined in PR #336 .

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
* Configurable status-query tool (sacct/squeue), retry attempts,
post-init settings validation, and optional efficiency reports with
configurable path and threshold.

* **Improvements**
* Cluster-aware status querying with dynamic tool selection and smart
fallbacks based on cluster MinJobAge; contextual warnings about
status-command choices; improved shutdown and robust log cleanup
(including empty-directory handling).

* **Chores**
  * Formatting/tooling config and minor style/readability tweaks.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
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---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

Author: cmeesters

pyproject.toml

@@ -33,6 +33,10 @@ pandas = "^2.2.3"
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
 
+[tool.black]
+line-length = 87
+target-version = ['py311']
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"