Recommend safe Bash permissions for Elixir mix commands in; Use when permission prompts slow workflow, "fix…
npx skills add https://github.com/oliver-kriska/claude-elixir-phoenix --skill phx-permissions
Scan recent session transcripts to find Bash commands you keep approving,
cross-reference with current settings.json, and recommend adding the missing ones.
Primary goal: Discover MISSING permissions from actual usage.
Secondary goal: Clean up redundant/garbage entries.
$elixir-phoenix:phx-permissions [--days=14] [--dry-run] — Scans session JSONL files, finds uncovered Bash commands, classifies risk, and recommends settings.json changes. Use --dry-run to
preview without writing.
$ARGUMENTS — --days=N (default: 14), --dry-run (preview only).
rm, sudo, kill, curl|sh, mix ecto.reset, git push --force, chmod 777| Level | Examples | Action |
|-------|----------|--------|
| GREEN | ls, cat, grep, tail, which, mkdir, cd, mix test/compile/credo/format, git status/log/diff | Auto-recommend |
| YELLOW | git add/commit/push, mix ecto.migrate, mix deps.get, npm install, docker build/run, source, mise exec | Recommend with note |
| RED | rm -rf, sudo, kill, curl|sh,mix ecto.reset/drop,git push --force,git reset --hard | Never recommend |
Run the extraction script from references/extraction-script.md.
This scans all project JSONL files from the last N days, checks each Bash command
against current settings.json patterns, and reports uncovered commands with counts.
IMPORTANT: Run this FIRST. Do NOT skip to settings cleanup.
For each uncovered command from Step 1 output:
Bash(base_command *) format(use SPACE before *, NOT colon — :* is deprecated)
mkdir -p (94x) → Bash(mkdir *)mise exec (39x) → Bash(mise *)tail -5 (20x) → Bash(tail *)Bash(done), Bash(fi),Bash(__NEW_LINE_*), partial heredocs, entries covered by broader patterns
:* patterns — replace any Bash(name:*) with Bash(name *)(space before *). The :* suffix is deprecated and may not match reliably
Present a combined table:
## Permission Recommendations (last N days)
### ADD — Missing permissions (from session scan)
| Pattern to Add | Times Used | Risk | Example |
|...
### REMOVE — Redundant/garbage entries
| Entry | Reason |
|...
### RED — Require manual approval (not adding)
| Command | Count | Risk |
|...
--dry-run)Walk through findings interactively using AskUserQuestion. Present items
in batches by risk level, starting with GREEN (safest):
Batch 1 — GREEN items (read-only, tests, safe tools):
Use AskUserQuestion with options:
Batch 2 — YELLOW items (write ops, need caution):
Always show individually — one AskUserQuestion per item with options:
Batch 3 — REMOVE candidates (garbage/redundant):
Use AskUserQuestion with options:
Track approved items in a list. After triage, show final summary of
what will be added/removed and ask for confirmation.
Merge approved additions into ~/.claude/settings.json under permissions.allow.
Remove approved garbage entries. Report final counts.
The plugin's workflow writes to .claude/plans/, .claude/solutions/, and
.claude/reviews/. If these aren't covered, $elixir-phoenix:phx-compound and review agents
get write-blocked mid-workflow. Recommend (GREEN):
Write(.claude/plans/), Write(.claude/solutions/), Write(.claude/reviews/**).
references/risk-classification.md — Full classification rulesreferences/settings-format.md — Permission pattern formatLong mix output flooding context? $elixir-phoenix:phx-mix-compression installs rtk filters
that compress mix test/credo/dialyzer/compile output before it reaches the
transcript (5-15% token savings on mix-heavy sessions).
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.
Build and distribute Expo development clients locally or via TestFlight
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Take oliver-kriska/claude-elixir-phoenix-phx-permissions from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.
The instructions reference npm.
Without those the skill loads but fails at the first command.