Add docstrings to all functions and methods and other cleanup

[wtgee]

I had my pycharm Junie agent go through and add docstrings where missing. There should not be any code or functionality changes.

• Changes protobuf dependency. (⚠️ not tested ⚠️)
• Removes unused alignment method and renames current methods so quick-alignment now has alignment as an alias.
• Adds Junie guidelines to the repo.

[Copilot]

Pull Request Overview

This PR adds comprehensive docstrings to functions and methods across the PANOPTES POCS codebase to improve code documentation and usability. The effort was done by a Junie agent to systematically document missing docstrings throughout the project.

Key changes include:

• Addition of module-level docstrings to explain the purpose of each module
• Function and method docstrings with proper parameter descriptions and return value documentation
• Property getter/setter documentation for better API clarity

Reviewed Changes

Copilot reviewed 89 out of 89 changed files in this pull request and generated 2 comments.

File	Description
src/panoptes/pocs/**/*.py	Addition of comprehensive docstrings to all undocumented functions, methods, and modules
pyproject.toml	Removed specific protobuf version constraint
.junie/guidelines.md	Added project guidelines for Junie agent

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

[codecov]

Codecov Report

❌ Patch coverage is 11.11111% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.46%. Comparing base (f667c04) to head (fc1638b).
⚠️ Report is 13 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/panoptes/pocs/utils/cli/main.py	0.00%	22 Missing ⚠️
src/panoptes/pocs/mount/mount.py	0.00%	1 Missing ⚠️
src/panoptes/pocs/utils/cli/network.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1377      +/-   ##
===========================================
+ Coverage    63.98%   64.46%   +0.48%     
===========================================
  Files          103      103              
  Lines         9451     9368      -83     
  Branches       831      831              
===========================================
- Hits          6047     6039       -8     
+ Misses        3263     3188      -75     
  Partials       141      141              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.