doc: Fix references

[dweindl]

Fix many of the cross-references broken during the recent renaming and moving of objects.
Also fixes some intersphinx references that never worked.

Related to #3062.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.60%. Comparing base (d578a31) to head (7c01e6b).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3097      +/-   ##
==========================================
- Coverage   78.25%   77.60%   -0.66%     
==========================================
  Files         315      315              
  Lines       20466    20466              
  Branches     1500     1500              
==========================================
- Hits        16016    15882     -134     
- Misses       4441     4575     +134     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.73% <ø> (ø)
cpp_python	37.73% <ø> (ø)
petab	46.46% <ø> (ø)
petab_sciml	13.79% <ø> (ø)
python	70.37% <ø> (ø)
sbmlsuite-jax	?

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Files with missing lines	Coverage Δ
include/amici/model.h	78.04% <ø> (ø)
...hon/sdist/amici/importers/petab/_petab_importer.py	86.78% <ø> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.64% <ø> (ø)
python/sdist/amici/importers/utils.py	83.33% <ø> (-2.71%)	⬇️
python/sdist/amici/sim/sundials/_debugging.py	78.57% <ø> (ø)
python/sdist/amici/sim/sundials/_swig_wrappers.py	100.00% <ø> (ø)
python/sdist/amici/sim/sundials/petab/_v2.py	94.06% <ø> (ø)
...n/sdist/amici/sim/sundials/petab/v1/_conditions.py	98.33% <ø> (ø)
.../sdist/amici/sim/sundials/petab/v1/_simulations.py	94.73% <ø> (ø)
...on/sdist/amici/sim/sundials/petab/v1/_simulator.py	96.66% <ø> (ø)
... and 1 more

... and 4 files with indirect coverage changes

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