feat: add input validation for setup tools

[galjos]

Recreates #322 after #324 restored dev. This PR requires review before merge.

Summary

• add stable help, version, capabilities, and validation CLI contracts
• return file- and line-aware diagnostics for parser and cross-field errors
• install external-QM scripts, references, and Slakos assets relocatably
• harden temperature, progress, and cell-list edge cases

Integration

• PQSetup uses --capabilities=json for version, build, runner, default, and range discovery
• PQSetup uses --validate run.in --format=json for authoritative checks
• PQSetup keeps local v0.6.4 checks when PQ does not advertise this contract

Validation

• recreated source tree exactly matches the tested feat: add input validation for setup tools #322 head
• shared Debug: 153/153
• static Release/Singularity: 153/153
• shared Release/ASE: 154/154, including staged Slakos install
• the identical tree passed the full GitHub matrix and both coverage gates

[codecov]

Codecov Report

❌ Patch coverage is 91.62861% with 55 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.31%. Comparing base (262484e) to head (5b3911d).

Files with missing lines	Patch %	Lines
src/input/inputFileReader.cpp	67.44%	14 Missing ⚠️
src/input/inputValidation.cpp	93.79%	8 Missing ⚠️
src/output/references/referencesOutput.cpp	83.33%	7 Missing ⚠️
...c/input/inputFileParser/convergenceInputParser.cpp	89.36%	5 Missing ⚠️
src/input/inputFileParser/hybridInputParser.cpp	81.81%	4 Missing ⚠️
src/input/commandLineArgs.cpp	95.74%	0 Missing and 2 partials ⚠️
src/input/inputFileParser/manostatInputParser.cpp	88.88%	2 Missing ⚠️
src/input/inputFileParser/optInputParser.cpp	93.10%	2 Missing ⚠️
src/setup/thermostatSetup.cpp	60.00%	2 Missing ⚠️
src/utilities/executablePath.cpp	85.71%	2 Missing ⚠️
... and 7 more

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #325      +/-   ##
==========================================
+ Coverage   89.81%   90.31%   +0.50%     
==========================================
  Files         293      293              
  Lines       11420    11787     +367     
  Branches     3600     3772     +172     
==========================================
+ Hits        10257    10646     +389     
+ Misses       1122     1099      -23     
- Partials       41       42       +1     

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[pq-perf-bot]

⚡ Performance (instruction count) — ✅ no regressions

per-benchmark breakdown

benchmark	base Ir	PR Ir	Δ
bondedForces	41.46M	41.46M	-0.00%	✅
boxTransforms	10.67M	10.67M	-0.00%	✅
constraints	11.38M	11.38M	-0.00%	✅
coulombKernel	5.80M	5.80M	+0.00%	✅
forceKernel	15.33M	15.33M	+0.00%	✅
integrator	32.17M	32.17M	-0.00%	✅
kinetics	9.53M	9.53M	-0.00%	✅
linearAlgebra	2.07M	2.07M	+0.00%	✅
nonCoulombPairs	5.48M	5.48M	-0.00%	✅
shiftVector	5.81M	5.81M	-0.00%	✅
virial	11.64M	11.63M	-0.07%	✅

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

[galjos]

Superseded by focused issue/PR pairs. Each PR is ready for peer review and requests ape33 and 97gamjak.

CLI and validation

• Add a stable PQ command-line contract #326 → feat: add PQ CLI contract #327 — CLI contract
• Validate input files without starting a simulation #328 → feat: validate PQ inputs #337 — portable input validation
• Reject malformed numeric input values consistently #331 → fix: validate numeric input values #336 — numeric parsing and ranges
• Reject inconsistent input setting combinations #338 → fix: validate input configuration #347 — cross-field validation
• Catalog bundled external QM scripts #356 → feat: catalog external QM scripts #364 — external-QM script catalog
• Expose validated input constraints in PQ capabilities #354 → feat: expose validated input constraints #370 — capability constraints
• Warn when control coupling is effectively disabled #371 → feat: warn about disabled control coupling #372 — disabled-coupling warnings
• Validate installed resources referenced by PQ inputs #357 → feat: validate installed input resources #373 — installed-resource validation

Runtime correctness

• Reject failed or stale external QM results #333 → fix: reject failed external QM results #335 — external-QM result and failure guards
• Quote external-QM command paths safely #362 → fix: quote external QM paths #363 — external-QM path quoting
• Fix ParameterFileReader destruction on AppleClang #339 → fix: define parameter reader destructor out of line #340 — ParameterFileReader lifetime fix
• Complete single-step progress bars #344 → fix: complete single-step progress bars #349 — single-step progress
• Handle zero-temperature velocity rescaling explicitly #345 → fix: handle zero-temperature rescaling #350 — zero-temperature rescaling
• Reach the exact target for partial-interval temperature ramps #341 → fix: complete partial temperature ramps #351 — exact partial temperature ramps
• Reject invalid cell-list dimensions before allocation #346 → fix: validate cell-list dimensions #348 — cell-list sizing guards
• Reject directories where PQ expects regular files #374 → fix: reject directories as input files #375 — regular-file checks

Installation and data

• Make CMake install-prefix overrides relocatable #332 → fix: make install destinations relocatable #334 — relocatable install destinations
• Remove test-only dependencies from production targets #352 → build: remove test runtime dependencies #353 — test/runtime dependency cleanup
• Locate runtime data relative to the PQ executable #358 → feat: add executable path utility #365 — executable-path utility
• Install and use PQ reference data #359 → fix: install reference data #366 — reference-data install
• Fail clearly when reference data cannot be read or written #355 → fix: fail on reference I/O errors #369 — reference I/O errors
• Install and resolve bundled external-QM scripts #360 → fix: install bundled QM scripts #367 — bundled QM scripts
• Pin, validate, and install bundled Slater-Koster data #361 → fix: install bundled Slakos data #368 — Slakos data

Documentation

• Correct the documented manostat relaxation default #342 → docs: correct manostat relaxation default #343 — manostat default

Suggested stack order:

• fix: reject failed external QM results #335 → fix: quote external QM paths #363
• fix: validate numeric input values #336 → fix: validate input configuration #347
• feat: add PQ CLI contract #327 → feat: validate PQ inputs #337 → feat: catalog external QM scripts #364 → feat: expose validated input constraints #370 / feat: warn about disabled control coupling #372 / feat: validate installed input resources #373
• fix: make install destinations relocatable #334 → feat: add executable path utility #365 → fix: install reference data #366 → fix: install bundled QM scripts #367 → fix: install bundled Slakos data #368
• fix: install reference data #366 → fix: fail on reference I/O errors #369

#370 also waits for #336 and #347. #373 also waits for #365, #367, and #368 and needs its temporary executable-path helper removed after #365 lands.

Whitespace-only changes and the incorrect t_relaxation = 1.0 ps documentation change were intentionally not carried forward.