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Remove outdated docs pages and fix the build warnings (#92)

* Remove outdated docs pages and fix the build warnings

Building the docs on master produces 88 warnings and errors. Most of them
trace back to pages that document an API which no longer exists, or to
copy-paste between the three module folders. This clears them out.

Removed, because they document the pre-saenopy workflow of handing the
solver a mesh as .txt files. Solver.setNodes, setTetrahedra,
setBoundaryCondition and loadMeshFromFile do not exist in the code any more:

  mesh.rst and its nodes.txt / connectivity.txt / constraint_*.txt /
  measured_displacement.txt, boundarycondition.ipynb, macrorheology.py,
  and the root interface.rst

None of these were reachable from the navigation — they were in no toctree,
so they were only findable by search or a direct link. mesh.rst also embedded
an interactive 3D viewer pointing at _static/vector_data2, which is not in
the repo; that embed is a 404 on the live site today. The viewer sources
under _static/js went with it, since nothing else used them.

Also removed: simplepython.tpl and convert_notebooks.bat, a notebook
conversion step nothing references.

Fixed:

- 2.5D Spheroid and 2.5D Orientation listed auto_examples in their toctree,
  but sphinx-gallery is only configured for 3d_tfm/examples and both folders
  hold no example scripts, so the entry silently vanished. The toctree entry
  is gone and the modules now say where their example data actually lives.
- Both of their api.rst files were verbatim copies of the 3D TFM one and
  re-documented saenopy.solver.Solver under the wrong module, which alone
  caused about 30 duplicate-object warnings. They now describe what is
  actually available.
- parameters_material.rst used Markdown tables inside RST. They render as
  loose pipes and dashes on the live site today. Rewritten as list-tables,
  with the parameter meanings taken from the SemiAffineFiberMaterial
  docstring and the one collagen... (continued)

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Source Files on job 30659045240.1