chore: deprecate manifest argument and remove deprecated methods

[jacobrkerstetter]

Description

• Deprecating the custom manifest path argument on the Discovery launcher per Matteo's request.
• Deprecate the launch_modeler_with_geometry_service() method and rename to launch_modeler_with_dms() as this was confusing to many users.
• Removing the run_discovery_script_file() and save() methods as they were deprecated for removal in 0.17.0.

Issue linked

Checklist

• I have tested my changes locally.
• I have added necessary documentation or updated existing documentation.
• I have followed the coding style guidelines of this project.
• I have added appropriate unit tests.
• I have reviewed my changes before submitting this pull request.
• I have linked the issue or issues that are solved to the PR if any.
• I have assigned this PR to myself.
• I have added the minimum version decorator to any new backend method implemented.
• I have made sure that the title of my PR follows Conventional commits style (e.g. feat: extrude circle to cylinder)

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 0 complexity · 2 duplication

Metric	Results
Complexity	0
Duplication	2

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.76%. Comparing base (ad6ea32) to head (9aadb4e).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3118      +/-   ##
==========================================
- Coverage   93.79%   93.76%   -0.03%     
==========================================
  Files         195      195              
  Lines       18171    18164       -7     
==========================================
- Hits        17043    17031      -12     
- Misses       1128     1133       +5     

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