Fix version.txt paths

[dweindl]

Fix version.txt paths and MANIFEST.in after rearranging files (#3060).

Fixes installation failures from sdist (https://github.com/AMICI-dev/AMICI/actions/runs/19534015315/job/55923610379).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.52%. Comparing base (63f2e78) to head (fda41a6).
⚠️ Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3067      +/-   ##
==========================================
- Coverage   78.16%   77.52%   -0.64%     
==========================================
  Files         313      313              
  Lines       20656    20656              
  Branches     1500     1499       -1     
==========================================
- Hits        16145    16013     -132     
- Misses       4502     4634     +132     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.61% <ø> (ø)
cpp_python	37.25% <ø> (ø)
petab	45.86% <ø> (ø)
petab_sciml	13.82% <ø> (ø)
python	70.21% <ø> (ø)
sbmlsuite-jax	?

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see 5 files with indirect coverage changes

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