fix(docker): combine pixi installs into single RUN to prevent disk-full (#206)

## Summary
- Combines the three separate `RUN pixi install` commands back into a
single `RUN`
- Separate RUNs create overlay layers that duplicate shared conda
packages (numpy, CUDA libs, etc.) across environments -- measured **~37
GB** (3 layers) vs **~14 GB** (1 layer)
- `ubuntu-latest` non-deterministically provisions runners with 72 GB or
145 GB disks. On 72 GB runners, the split-RUN approach exceeds available
space during build

### Root cause investigation
The split was introduced in #204 for better layer caching. However, the
three pixi environments share many conda packages, and overlay layers
store full copies of files per layer. This ~23 GB overhead pushes the
build past the disk limit on smaller runners.

Disk usage measured via `df -h` inside Docker build steps:

| Metric | Split RUN (3 layers) | Single RUN (1 layer) |
|--------|---------------------|---------------------|
| boltz | 8 GB | 8 GB |
| protenix | 12 GB (new layer) | 4 GB (shared pkgs deduped) |
| rf3 | 12 GB (new layer) | 2 GB (shared pkgs deduped) |
| **Total pixi disk** | **~37 GB** | **~14 GB** |

## Test plan
- [x] Verified split-RUN fails on 72 GB runners (jobs 70663224672,
70670232201)
- [x] Verified single-RUN disk usage via df -h debugging (job
70682099334)
- [x] Confirmed checkpoint image unchanged since March 25 (same SHA
across all builds)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **Chores**
* Streamlined the deployment build process by consolidating multiple
environment setup commands into a single optimized layer, resulting in
improved build performance, reduced container image overhead, better
dependency caching efficiency, and enhanced operational efficiency
during containerization and deployment cycles while maintaining full
functionality.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: Abdelsalam-Abbas

Dockerfile

@@ -113,10 +113,13 @@ COPY --from=diffuseproject/sampleworks-checkpoints:latest /checkpoints/ /checkpo
 # ============================================================================
 # Install all three environments: boltz, protenix, rf3
 # ============================================================================
-# Split into separate layers so changing one env doesn't invalidate the others
-RUN pixi install -e boltz --frozen
-RUN pixi install -e protenix --frozen
-RUN pixi install -e rf3 --frozen
+# IMPORTANT: Must be a single RUN — separate RUNs create overlay layers that
+# duplicate shared conda packages (numpy, CUDA libs, etc.), using ~37 GB vs
+# ~14 GB in a single layer. This difference causes disk-full failures on
+# smaller CI runners (ubuntu-latest can be 72 GB or 145 GB).
+RUN pixi install -e boltz --frozen && \
+    pixi install -e protenix --frozen && \
+    pixi install -e rf3 --frozen
 
 # ============================================================================
 # Pre-compile CUDA extensions to avoid JIT compilation at runtime