docs: add DEV_NOTES.md with GPU/dependency setup issues

Author: parallelArchitect

DEV_NOTES.md

@@ -0,0 +1,39 @@
+# Development Notes
+
+Setup friction encountered on this fork during GPU development — kept
+here separately so the main README stays clean. Not universal microsim
+guidance, just what was hit on this machine.
+
+## GPU backend (cupy) setup
+
+1. **numpy version conflict** — microsim's metadata pins `numpy<2.0`, but
+   `cupy-cuda12x` requires `numpy>=2.0`. In practice, numpy 2.4.6 worked
+   fine at runtime with this version of microsim despite the metadata
+   warning — if `pip` flags the conflict, it's likely safe to ignore,
+   but verify by running a real simulation before trusting it.
+
+2. **CUDA headers not found** (`RuntimeError: Failed to find CUDA headers`)
+   — if your system has multiple CUDA toolkit installs (common after
+   driver updates over time), cupy's JIT compiler may not find headers
+   even with `CUDA_PATH` set correctly. Installing the toolkit extra
+   directly into the venv sidesteps the problem:
+```bash
+   pip install "cupy-cuda12x[ctk]"
+```
+
+3. **zarr / numcodecs mismatch** (`ImportError: cannot import name
+   'cbuffer_sizes' from 'numcodecs.blosc'`) — zarr 2.17.x expects an
+   older numcodecs API:
+```bash
+   pip install "numcodecs<0.13"
+```
+
+4. **COSEM data fetching** — loading real segmentation data (e.g. the
+   `cosem` example) requires the optional extra:
+```bash
+   pip install "microsim[cosem]"
+```
+
+None of these are bugs in microsim itself, except where already filed
+as upstream PRs (#140, #141) — mostly environment/dependency friction
+from multiple existing CUDA/Python installs on a dev machine.