Delete code previously marked for deprecation

[keileg]

Proposed changes

Deleted the following that has long been marked for deprecation:

1. Utility functions in FractureNetwork3d
2. The module coarsening together with tests
3. Functionality for MVEM/MFEM to compose mixed-dimensional discretizations using the old assembler-style techniques.

Types of changes

What types of changes does this PR introduce to PorePy?
Put an x in the boxes that apply.

• Minor change (e.g., dependency bumps, broken links).
• Bugfix (non-breaking change which fixes an issue).
• New feature (non-breaking change which adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• Testing (contribution related to testing of existing or new functionality).
• Documentation (contribution related to adding, improving, or fixing documentation).
• Maintenance (e.g., improve logic and performance, remove obsolete code).
• Other: Deprecations

Checklist

Put an x in the boxes that apply or explain briefly why the box is not relevant.

• The documentation is up-to-date.
• Static typing is included in the update.
• This PR does not duplicate existing functionality.
• The update is covered by the test suite (including tests added in the PR).
• If new skipped tests have been introduced in this PR, pytest was run with the --run-skipped flag.

[keileg]

@jwboth I realized that we actually use the coarsening module (which has long been deprecated) for testing of the exporter applied to polytopal grids. Is this something we need, and are there ways in which we can circumvent this (I can implement if you can give me some guidance)?

Of course we can un-deprecate the module, but there is a certain cost in maintenance to that code, so I don't want to do this if there are other ways.