[DOCUMENTATION]: Reconcile SKILL.md with PR #112 changes (AETHERSCAN_EXTRA_BINDS, .env example)

[claude]

Context

PR #112 (merged as 13eb22c) added a new AETHERSCAN_EXTRA_BINDS env var to utils/run_container.sh, updated the README .env example block (reordered vars, added AETHERSCAN_EXTRA_BINDS), and updated the raw .h5 inference example to show the new var. KNOWN_ISSUES.md entry #16 was also added but neither CLAUDE.md nor the SKILL.md reference individual entries, so no drift there.

CLAUDE.md is unaffected — it doesn't restate any of the specific facts that changed.

.claude/skills/aetherscan-repo-context/SKILL.md has three drifts against the updated canonical docs (README.md):

Specific updates needed

SKILL.md edits (apply manually — .claude/ is read-only in CI)

Edit 1 — run_container.sh description (line 31): Add AETHERSCAN_EXTRA_BINDS to the description.

Old:

- **`utils/run_container.sh`** auto-detects apptainer vs singularity (Apptainer wins when both present), sets `--nv` for GPU passthrough, auto-loads `<repo>/.env`, and bind-mounts the repo + `AETHERSCAN_{DATA,MODEL,OUTPUT}_PATH` 1:1 so absolute paths persisted in the DB stay valid across host and container.

New:

- **`utils/run_container.sh`** auto-detects apptainer vs singularity (Apptainer wins when both present), sets `--nv` for GPU passthrough, auto-loads `<repo>/.env`, and bind-mounts the repo + `AETHERSCAN_{DATA,MODEL,OUTPUT}_PATH` 1:1 so absolute paths persisted in the DB stay valid across host and container. `AETHERSCAN_EXTRA_BINDS` (comma-separated host paths) appends additional 1:1 binds for data outside the standard dirs (e.g. raw `.h5` files under `/datag` for inference); the runtime's native `SINGULARITY_BIND` / `APPTAINER_BIND` still pass through and are additive.

Edit 2 — Raw .h5 inference example (lines 50-55): Add AETHERSCAN_EXTRA_BINDS prefix and update the comment to match README.md.

Old:

# Inference from raw .h5 (triggers energy-detection preprocessing)
./utils/run_container.sh python -m aetherscan.main inference \
    --inference-files complete_cadences_catalog.csv \
    --encoder-path /path/to/vae_encoder.keras \
    --rf-path /path/to/random_forest.joblib \
    --config-path /path/to/config.json

New:

# Inference from raw .h5 (triggers energy-detection preprocessing) — bind
# extra host paths if the .h5 files live outside the standard bind mounts
AETHERSCAN_EXTRA_BINDS=/datag ./utils/run_container.sh python -m aetherscan.main inference \
    --inference-files complete_cadences_catalog.csv \
    --encoder-path /path/to/vae_encoder.keras \
    --rf-path /path/to/random_forest.joblib \
    --config-path /path/to/config.json

Edit 3 — .env example block (lines 74-82): Add AETHERSCAN_EXTRA_BINDS and reorder to match README.md (path vars first, then extra binds, then Slack).

Old:

# .env example (Slack integration auto-disables if unset)
SLACK_BOT_TOKEN=your-slack-bot-token
SLACK_CHANNEL=your-slack-channel
# Defaults to /datax/scratch/zachy/{data|models|outputs}/aetherscan; CLI flags override
AETHERSCAN_DATA_PATH=/path/to/data
AETHERSCAN_MODEL_PATH=/path/to/models
AETHERSCAN_OUTPUT_PATH=/path/to/outputs

New:

# .env example
# Defaults to /datax/scratch/zachy/{data|models|outputs}/aetherscan; CLI flags override
AETHERSCAN_DATA_PATH=/path/to/data
AETHERSCAN_MODEL_PATH=/path/to/models
AETHERSCAN_OUTPUT_PATH=/path/to/outputs
# Optional: comma-separated extra host paths for run_container.sh to bind 1:1
AETHERSCAN_EXTRA_BINDS=/extra/host/paths
# Slack integration auto-disables if unset
SLACK_BOT_TOKEN=your-slack-bot-token
SLACK_CHANNEL=your-slack-channel

Instructions for @claude

Open a PR that Closes this issue. CLAUDE.md needs no changes. For SKILL.md:

1. Do NOT attempt to modify .claude/skills/aetherscan-repo-context/SKILL.md — it is read-only in CI.
2. Copy the three SKILL.md edits above verbatim into the PR body, followed by step-by-step instructions for a human to apply them: check out the PR branch locally (gh pr checkout <PR#>), make the listed edits to .claude/skills/aetherscan-repo-context/SKILL.md, commit, and push back to the branch for review & merge.
3. Tag @zachtheyek (code owner per CODEOWNERS) in the PR body to perform the local apply.

[claude]

PR #138 is up with the three verbatim SKILL.md edits and step-by-step instructions for applying them locally. @zachtheyek is tagged in the PR body to perform the apply.