Apply one rewrite-plan step at a time as small reviewable file edits, never rewriting whole files when a localised change suffices.
npx skills add https://github.com/nexu-io/open-design --skill patch-edit
Spec §20.3 / §21.3.2: code-migration / tune-collab cannot ship a
trustworthy diff when the agent rewrites whole files in one pass —
the reviewer can't audit the change. This atom enforces "one step
per turn, smallest possible localised edit".
plan/steps.json from rewrite-plan.iterations (the daemon's per-stage counter).code/index.json for the file's known imports + neighbours.The atom mutates files inside the project cwd via the file-edit tool.
After every iteration, it writes a per-step receipt:
project-cwd/
└── plan/
├── steps.json (status updated: 'pending' → 'completed' | 'skipped')
└── receipts/
└── step-<id>.json # { files: ['...'], diffSummary, rationale, completedAt }
The atom completes when every step in plan/steps.json is in a
terminal state (completed / skipped) OR `iterations >=
OD_MAX_DEVLOOP_ITERATIONS`. Use:
{
"id": "patch-edit-loop",
"atoms": ["patch-edit"],
"repeat": true,
"until": "plan.steps.terminal === plan.steps.total || iterations >= 8"
}
files[].shell-tier file when the step's risk is not'high' or the user hasn't confirmed.
Implemented by the daemon runner in
apps/daemon/src/plugins/atoms/patch-edit.ts. It validates step ownership and
risk, applies unified diffs with atomic writes, and records receipts and
progress.
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 nexu-io/patch-edit 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.