refactor: remove engine dependency from FilesInputFileParser and upda…

[97gamjak]

…te related methods

[pq-perf-bot]

⚡ Performance (instruction count) — ✅ no regressions

per-benchmark breakdown

benchmark	base Ir	PR Ir	Δ
bondedForces	38.24M	38.24M	-0.00%	✅
boxTransforms	10.67M	10.67M	+0.00%	✅
constraints	10.91M	10.91M	-0.00%	✅
coulombKernel	5.80M	5.80M	+0.00%	✅
forceKernel	14.16M	14.16M	-0.00%	✅
integrator	32.44M	32.44M	+0.00%	✅
interWater	1681.40M	1681.40M	+0.00%	✅
kinetics	8.55M	8.55M	+0.00%	✅
linearAlgebra	2.08M	2.08M	+0.00%	✅
nonCoulombPairs	5.48M	5.48M	+0.00%	✅
shiftVector	5.81M	5.81M	+0.00%	✅
virial	10.44M	10.44M	+0.00%	✅

_{Deterministic callgrind instruction counts vs the base branch; gated at ±2%. Not wall-clock.}

[codecov]

Codecov Report

❌ Patch coverage is 94.73684% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 91.02%. Comparing base (f5667ee) to head (a8517a2).

Files with missing lines	Patch %	Lines
src/setup/intraNonBondedSetup.cpp	80.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #498      +/-   ##
==========================================
- Coverage   91.02%   91.02%   -0.01%     
==========================================
  Files         320      320              
  Lines       14563    14567       +4     
  Branches     4825     4828       +3     
==========================================
+ Hits        13256    13259       +3     
- Misses       1221     1222       +1     
  Partials       86       86              

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