Scrub internal references and add cluster config for open-source readiness

.claude/commands/add-model.md

@@ -45,12 +45,12 @@ Add a new model to this repository following all repo conventions.
 9. **Do not commit** large checkpoints, datasets, `.env` files, or tokens — document how users obtain them instead.
 
 10. **Git workflow** — always branch, never commit directly to `main`:
-    1. `git fetch origin && git checkout -b aaji/<model-slug> origin/main`
+    1. `git fetch origin && git checkout -b <your-username>/<model-slug> origin/main`
     2. Create all files, set scripts `chmod +x`.
     3. `git add <domain>/models/<slug>/` and commit.
-    4. `git push -u origin aaji/<model-slug>`
+    4. `git push -u origin <your-username>/<model-slug>`
     5. Open a PR with `gh pr create` targeting `main`.
-    6. After the PR is merged: `git checkout main && git pull origin main && git branch -D aaji/<model-slug>`.
+    6. After the PR is merged: `git checkout main && git pull origin main && git branch -D <your-username>/<model-slug>`.
 
 ## Model to add
 

.claude/commands/add-recipe.md

@@ -37,12 +37,12 @@ Create or improve a recipe (inference, fine-tune, eval, etc.) for a model alread
 6. **Do not commit** secrets, Hub tokens, large binaries, or datasets — point users to documented download steps.
 
 7. **Git workflow** — always branch, never commit directly to `main`:
-   1. `git fetch origin && git checkout -b aaji/<model-slug> origin/main`
+   1. `git fetch origin && git checkout -b <your-username>/<model-slug> origin/main`
    2. Create all files, set scripts `chmod +x`.
    3. `git add <domain>/models/<slug>/` and commit.
-   4. `git push -u origin aaji/<model-slug>`
+   4. `git push -u origin <your-username>/<model-slug>`
    5. Open a PR with `gh pr create` targeting `main`.
-   6. After the PR is merged: `git checkout main && git pull origin main && git branch -D aaji/<model-slug>`.
+   6. After the PR is merged: `git checkout main && git pull origin main && git branch -D <your-username>/<model-slug>`.
 
 ## Domain-specific checks
 

.claude/commands/init-cluster.md

@@ -0,0 +1,164 @@
+# Initialize local cluster configuration
+
+Detect the current cluster environment and create a `.cluster-config.yaml` file with site-specific settings. This file is gitignored and never committed.
+
+## Step 0 — Check if config already exists
+
+Check both locations in order:
+1. `.cluster-config.yaml` (repo root)
+2. `~/.config/ai4science-studio/cluster.yaml`
+
+If either exists, read it, show the user the current settings, and ask:
+- **Update** — re-run discovery and update the file
+- **Keep** — leave it as-is and exit
+
+If neither exists, proceed to Step 1.
+
+## Step 1 — Auto-discover cluster environment
+
+Run ALL of the following discovery commands silently (do not show raw output). Parse and store results for the questionnaire in Step 2.
+
+```bash
+# 1. Home directory (may not be /home/...)
+echo "$HOME"
+
+# 2. GPU architecture and count
+rocminfo 2>/dev/null | grep -oP 'gfx\d+' | sort -u
+rocm-smi --showproductname 2>/dev/null | head -20
+ls /dev/dri/renderD* 2>/dev/null | wc -l
+
+# 3. VRAM per GPU (MB → GB)
+rocm-smi --showmeminfo vram 2>/dev/null | grep "Total" | head -1
+
+# 4. ROCm version
+cat /opt/rocm/.info/version 2>/dev/null || rocminfo 2>/dev/null | grep -oP 'HSA Runtime Version:\s*\K.*'
+
+# 5. SLURM: available GPU partitions
+sinfo -h -o "%P %l %G %D" 2>/dev/null | grep -i gpu
+
+# 6. SLURM: user's accounts and associations
+sacctmgr show associations where user=$USER format=account%30,partition%30,qos%30 -n 2>/dev/null
+
+# 7. Container runtimes available
+which apptainer 2>/dev/null && apptainer --version
+which docker 2>/dev/null && docker --version 2>/dev/null
+docker info 2>/dev/null | grep -i "amd\|runtime"
+
+# 8. Common scratch / project directories
+for d in /scratch/$USER /scratch /lustre /gpfs /tmp/$USER; do
+    [[ -d "$d" ]] && echo "scratch: $d"
+done
+
+# 9. Internet connectivity from this node
+curl -s --connect-timeout 5 -o /dev/null -w "%{http_code}" https://huggingface.co 2>/dev/null
+
+# 10. Proxy settings
+echo "HTTP_PROXY=${HTTP_PROXY:-<unset>}"
+echo "HTTPS_PROXY=${HTTPS_PROXY:-<unset>}"
+
+# 11. Existing SIF files
+find "$HOME" /scratch /projects /opt -maxdepth 4 -name "*.sif" 2>/dev/null | head -20
+```
+
+## Step 2 — Present findings and ask user to confirm or choose
+
+Show the user a summary table of discovered values. For each category, present what was found and ask them to confirm or override.
+
+### Questions (use AskUserQuestion for multi-choice items)
+
+**Q1. GPU architecture** (auto-filled if detected)
+Show detected arch (e.g. "gfx942 — MI300X"). Ask only if detection failed:
+- MI300X (gfx942)
+- MI250X (gfx90a)
+- MI350X (gfx950)
+- MI210 (gfx90a)
+- MI100 (gfx908)
+
+**Q2. GPUs per node** (auto-filled from renderD count, default 8)
+Show detected count. Ask to confirm or override.
+
+**Q3. VRAM per GPU** (auto-filled if detected)
+Show detected value. Ask to confirm or override.
+
+**Q4. SLURM partition** (choose from discovered partitions)
+If multiple GPU partitions found, present them as multiple-choice.
+If only one, pre-fill and ask to confirm.
+If SLURM not available (e.g. Docker-only workstation), set to empty.
+
+**Q5. SLURM account** (choose from discovered accounts)
+If multiple accounts found, present them as multiple-choice.
+If only one, pre-fill and ask to confirm.
+If SLURM not available, set to empty.
+
+**Q6. Container runtime**
+Based on what's available:
+- **Apptainer** (if found — recommended for HPC)
+- **Docker** (if found)
+- **Both** (if both found — ask which is preferred)
+
+If Docker is available, also check for AMD Container Toolkit:
+- If `docker info` shows AMD runtime → set `gpu_method: amd-toolkit`
+- Otherwise → set `gpu_method: device-passthrough`
+
+**Q7. Scratch / working directory**
+Show discovered writable directories. Ask user to pick or provide their preferred scratch path for large files (SIF, overlays, datasets).
+
+**Q8. Internet access**
+Show result of connectivity test. Ask to confirm.
+If no internet, ask for proxy settings.
+
+**Q9. Config file location**
+- `.cluster-config.yaml` in this repo (recommended — per-checkout)
+- `~/.config/ai4science-studio/cluster.yaml` (user-level, shared across clones)
+
+## Step 3 — Write the config file
+
+Write the YAML config to the chosen location using the confirmed values. Use this structure:
+
+```yaml
+# AI4Science Studio — Local Cluster Configuration
+# Auto-generated by /init-cluster on <date>
+# Edit manually or re-run /init-cluster to update.
+
+slurm:
+  partition: "<confirmed partition>"
+  account: "<confirmed account>"
+  qos: ""
+
+paths:
+  home: "<$HOME value>"
+  scratch: "<confirmed scratch path>"
+  projects: ""
+  sif_cache: "<path where .sif files were found, or scratch/containers>"
+
+containers:
+  runtime: "<apptainer|docker>"
+  gpu_method: "<amd-toolkit|device-passthrough|rocm-flag>"
+
+gpu:
+  architecture: "<gfxNNN>"
+  count_per_node: <N>
+  vram_gb: <N>
+
+network:
+  internet_access: <true|false>
+  proxy: "<proxy URL or empty>"
+
+discovered_sifs:
+  # SIF files found during init (informational — not used by scripts)
+  # - /path/to/some.sif
+```
+
+After writing, confirm to the user:
+- File location
+- Summary of all settings
+- Remind them this file is gitignored and will never be committed
+- Tell them to re-run `/init-cluster` if they move to a different cluster
+
+## Step 4 — Show next steps
+
+Suggest what the user can do next:
+- Run a model: `/run-stormcast`, `/run-orbit2`, etc.
+- The run commands will read cluster config automatically for SLURM partition/account defaults
+
+$ARGUMENTS

.claude/commands/run-archesweather.md

@@ -2,6 +2,10 @@
 
 Guide the user through running ArchesWeather end-to-end on an AMD cluster.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.
@@ -52,7 +56,7 @@ Run these when the user chose **Auto-discover** for any question. Present the re
 ```bash
 find "$HOME" /scratch /projects /opt -maxdepth 4 -name "*.sif" 2>/dev/null | head -20
 ```
-Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix (e.g. `/shared/prerelease/home/…`).
+Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix.
 Filter results for SIF names containing `geoarches` or `rocm`. Verify with `apptainer inspect <sif>` if multiple candidates.
 
 **SLURM partition and account (Q6):**

.claude/commands/run-aurora.md

@@ -2,6 +2,10 @@
 
 Guide the user through running Aurora (0.1° resolution) end-to-end on an AMD cluster.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.

.claude/commands/run-gencast.md

@@ -2,6 +2,10 @@
 
 Guide the user through running GenCast end-to-end on an AMD cluster.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.

.claude/commands/run-gpmolformer.md

@@ -5,6 +5,10 @@
 
 Guide the user through running GP-MoLFormer on an AMD cluster via SLURM.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.
@@ -54,7 +58,7 @@ Run these when the user chose **Auto-discover** for any question. Present the re
 ```bash
 find "$HOME" /scratch /projects /opt -maxdepth 4 -name "*.sif" 2>/dev/null | head -20
 ```
-Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix (e.g. `/shared/prerelease/home/…`).
+Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix.
 Filter results for SIF names containing `rocm` or `pytorch`. Verify with `apptainer inspect <sif>` if multiple candidates.
 
 **SLURM partition and account (Q7):**

.claude/commands/run-hydragnn.md

@@ -2,6 +2,10 @@
 
 Guide the user through running HydraGNN predictive GFM inference on AMD GPUs.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire
 
 **Q0. Task**

.claude/commands/run-matey.md

@@ -2,6 +2,10 @@
 
 Guide the user through training or inference with MATEY on AMD GPUs.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire
 
 **Q0. Task**

.claude/commands/run-mattergen.md

@@ -2,6 +2,10 @@
 
 Guide the user through running MatterGen end-to-end on an AMD cluster via SLURM or Docker.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers before proceeding.
@@ -44,7 +48,7 @@ Run these when the user chose **Auto-discover** for any question. Present the re
 ```bash
 find "$HOME" /scratch /projects /opt -maxdepth 4 -name "*.sif" 2>/dev/null | head -20
 ```
-Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix (e.g. `/shared/prerelease/home/…`).
+Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix.
 Filter results for SIF names containing `rocm` or `pytorch`. Verify with `apptainer inspect <sif>` if multiple candidates.
 
 **SLURM partition and account (Q5):**

.claude/commands/run-neuralgcm.md

@@ -2,6 +2,10 @@
 
 Guide the user through running NeuralGCM end-to-end on an AMD cluster via Docker or SLURM.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.

.claude/commands/run-orbit2.md

@@ -2,6 +2,10 @@
 
 Guide the user through running ORBIT-2 end-to-end on an AMD cluster via SLURM.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.
@@ -61,7 +65,7 @@ Run these when the user chose **Auto-discover** for any question. Present the re
 ```bash
 find "$HOME" /scratch /projects /opt -maxdepth 4 -type d -name "ORBIT-2" 2>/dev/null | head -20
 ```
-Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix (e.g. `/shared/prerelease/home/…`).
+Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix.
 Look for a directory containing `src/` and `examples/` subdirectories to confirm it is a valid ORBIT-2 clone.
 
 **SIF files (Q2):**

.claude/commands/run-panguweather.md

@@ -2,6 +2,10 @@
 
 Guide the user through running PanguWeather end-to-end on an AMD cluster.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.

.claude/commands/run-reinvent4.md

@@ -4,6 +4,10 @@ Guide the user through running REINVENT4 transfer learning for molecular design
 
 > **Research / engineering use only.** Not for clinical or diagnostic use.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire
 
 **Q0. TOML config**

.claude/commands/run-semlaflow.md

@@ -4,6 +4,10 @@ Guide the user through generating 3D molecular structures with SemlaFlow on AMD
 
 > **Research / engineering use only.** Not for clinical or diagnostic use.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire
 
 **Q0. Checkpoint path**

.claude/commands/run-stormcast.md

@@ -2,6 +2,12 @@
 
 Guide the user through running StormCast end-to-end on an AMD cluster via SLURM.
 
+## Step 0 — Cluster config check
+
+Before starting, check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first to auto-discover the cluster environment.
+
+If a config exists, read it and pre-fill Q0 (runtime), Q6 (partition/account) from the saved values. Still present them to the user for confirmation but show the saved defaults.
+
 ## Step 1 — Questionnaire (ask ALL questions before doing anything)
 
 Ask the user the following questions. Do not assume any defaults. Wait for answers to all questions before proceeding.
@@ -50,7 +56,7 @@ Run these when the user chose **Auto-discover** for any question. Present the re
 ```bash
 find "$HOME" /scratch /projects /opt -maxdepth 4 -name "*.sif" 2>/dev/null | head -20
 ```
-Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix (e.g. `/shared/prerelease/home/…`).
+Use `$HOME` (not `/home`) so the search works when the home directory is under a non-standard prefix.
 Filter results for SIF names containing `rocm` or `pytorch`. Verify with `apptainer inspect <sif>` if multiple candidates.
 
 **Overlay images (Q2):**

.claude/commands/run-swinunetr.md

@@ -4,6 +4,10 @@ Guide the user through training or inference with SwinUNETR on AMD GPUs.
 
 > **Research / engineering use only.** Not for clinical or diagnostic use.
 
+## Step 0 — Cluster config check
+
+Check if `.cluster-config.yaml` (repo root) or `~/.config/ai4science-studio/cluster.yaml` exists. If neither exists, run the `/init-cluster` flow first. If a config exists, read it and pre-fill container runtime and SLURM partition/account from saved values.
+
 ## Step 1 — Questionnaire
 
 **Q0. Task**