Make ProtoEvo runnable on modern JDKs + usability and NN fixes

[ApocalypseGamer1]

Summary

This PR contains a batch of fixes I made to get the project building and running on a fresh modern setup, plus a few quality-of-life and correctness fixes I hit along the way. All changes preserve existing behavior at default settings; new toggles default off and existing UI is unchanged unless you press a new hotkey or click the new button.

Build / launch fixes (without these, the project does not run at all on a fresh modern JDK)

• core/build.gradle, desktop/build.gradle: lower sourceCompatibility from 23 to 21. JDK 21 is the latest installable LTS via winget; few users have JDK 23 lying around.
• desktop/build.gradle: remove --add-modules jdk.incubator.foreign --illegal-access=permit from jvmArgs. Both flags were removed in JDK 17+; their presence prevented launch on any modern JVM.
• Three GLSL fragment shaders mixed int * float (int filter_radius = 8; ... filter_radius * skipX), which strict drivers reject — the game crashed at first sim creation. Promote filter_radius to float:
  • assets/shaders/pause/fragment.glsl
  • assets/shaders/chemical/fragment.glsl
  • assets/shaders/blur/fragment.glsl
• Added a run.bat so the project can be launched without manual PATH setup.

Stability fixes (real bugs)

PlotGrid infinite loop — freezes the entire window

StatsGraphsScreen.refreshPlot calls setMajorTicks(range/5, ...). On a fresh sim with one or two stat snapshots, range is 0, so the major-tick step is 0. Then drawAxis does:

for (float x = 0; x <= xMax; x += xMajorTick) { ... }

x += 0 never advances. The render thread loops forever inside GlyphLayout.calculateWidths, allocating tick-label glyph buffers, and the LWJGL window goes "Not Responding". Confirmed with jhsdb jstack — main was stuck in PlotGrid.drawAxisXTickLabel. Fix:

• Sanitize tick steps at the setters (non-finite or <= 0 → 1.0).
• Hard cap of 200 ticks per axis loop as a second line of defense.

Simulation.run busy-wait

while (simulate) { if (paused) continue; ... } pinned a full CPU core whenever paused, starving the render thread. Replaced with Thread.sleep(20) while paused.

REPL.run null-line spam

bufferRead.readLine() returns null when stdin closes (e.g. launched via javaw). The old code did line.equals("\n") → NPE → caught generically → tight loop re-printing Cannot invoke "String.equals(Object)" because "line" is null. Now it cleanly exits the REPL on EOF and skips empty lines.

Time controls — variable speed without breaking physics

Simulation.update: when timeDilation > 1, run that many physics substeps per render frame at the original safe dt, instead of multiplying dt directly. Lets the user run the sim at e.g. 16× without protozoa tunneling through rocks. Capped at 64 substeps/frame to prevent the thread locking up; fractional values handled with a partial last step.

New hotkeys (SimulationKeyboardControls):

• ] — 2× faster (steps 0.0625, 0.125, ..., 32, 64)
• [ — 2× slower
• \ — reset to 1.0×

Current speed is printed to console.

Performance toggles

EnvironmentRenderer now exposes renderChemicals / renderShadows flags. The chemical-field overlay (ChemicalsRenderer.render) and the baked shadow texture (LightRenderer.render) are gated on them — both are screen-filling fragment passes that dominate GPU cost on weak hardware. New SimulationScreen.toggleLowDetailMode() flips both together.

• F10 — toggle low-detail (both)
• F11 — toggle chemicals only
• New top-bar button (left side, help_icon.png as a stand-in — feel free to swap to a better icon).

Neural-network mutation fix (high-impact correctness fix)

SynapseGene.cloneWithMutation previously did a full re-roll on every weight mutation:

newGene.weight = randomInitialWeight();   // uniform [-1, 1]

This makes fine-tuning impossible — every mutation is a discontinuous jump, so a population can never converge on good weights. Standard NEAT explicitly recommends the opposite: 90% small-Gaussian perturbation, ~10% full re-roll. Implemented exactly that, with weights clamped to [-4, 4] to prevent runaway random walk.

Also removed a redundant second setGRNInputs() call after network.tick() in GeneExpressionFunction.tick — the second call was wasted work and got overwritten on the next tick.

Genetic clusters viewer (new feature)

Implemented NetworkGenome.distance() (was a stub returning 0) using the standard NEAT compatibility distance: c1*E/N + c2*D/N + c3*Wbar.

New GeneticClustersScreen is a snapshot view of living protozoa, grouped by greedy speciation against the distance threshold (1.5). Each cluster row shows: color swatch (mean cell color), population, avg generation, avg energy, avg health, avg age. Bounded: 250 cells sampled, 40 clusters tracked, 30 displayed.

Reachable from the simulation top-bar (right side, multicell icon). Clusters and tick threshold are both private static final constants near the top of the file — easy to tune.

The screen is intentionally minimal (no FBO, no own SpriteBatch, no own ShaderProgram, no worker thread) after an earlier fancier version sometimes hung — that turned out to be the unrelated PlotGrid bug above, but the simpler implementation is also less surprising.

Notes for reviewers

• Saves directory layout, save format, and existing settings YAML are unchanged.
• All new UI is opt-in via hotkey or button; no existing controls are remapped.
• I deliberately did not touch CUDA / JCuda paths. Project still builds + runs without CUDA installed.
• Plant-evolution path still appears to crash separately (mentioned by the user mid-development); I did not investigate further. Not addressed here.

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