How do I install the Doctor skill?

Run npx skillmds@latest add stencila/doctor in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Doctor safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Doctor?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Doctor free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Doctor?

stencila (@stencila) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Doctor by stencila — Agent Skill

Name: Doctor
Author: stencila

File contents

/stencila:doctor

Diagnose the Stencila installation and workspace. Report findings as a short summary, not raw command output.

1. Resolve the CLI

Use the first of these that exists (the same ladder the plugin's SessionStart hook uses — if session context already reports a resolved path, use that and skip to step 2):

The path in the plugin's stencila_path setting: ${CLAUDE_PLUGIN_OPTION_STENCILA_PATH} (if set and not the default stencila)
./target/debug/stencila (when working in the Stencila source repo)
stencila on PATH (command -v stencila)
/usr/local/bin/stencila, ~/.local/bin/stencila, ~/.cargo/bin/stencila

If no CLI is found: report that Stencila is not installed and give the platform-appropriate install command —

macOS / Linux: curl -LsSf https://stencila.io/install.sh | bash
Windows: download the ZIP for the latest release from https://github.com/stencila/stencila/releases

Offer to run the installer, but never run it unprompted — wait for the user to say yes. Then stop; the remaining checks need a CLI.

2. Run the checks

With <stencila> as the resolved path, run (all with NO_COLOR=1 and --yes):

NO_COLOR=1 <stencila> --version --yes           # version (plugin tested against 2.14)
NO_COLOR=1 <stencila> upgrade --check --yes     # available upgrade (does NOT install)
NO_COLOR=1 <stencila> kernels list --yes        # execution kernels and availability
NO_COLOR=1 <stencila> linters list --yes        # linters
NO_COLOR=1 <stencila> tools list --yes          # external tools (pandoc, chrome, etc.)

Also check the workspace: does stencila.toml (or stencila.local.toml) exist in this or an ancestor directory? If yes, run NO_COLOR=1 <stencila> status --no-remotes --yes for tracked-document status.

3. Report

Summarise in a few lines:

Resolved CLI path and version; warn (do not fail) if the version is below 2.14, and mention stencila upgrade if an upgrade is available — do not run it without being asked.
Kernels relevant to the user's documents that are unavailable (e.g. R documents but no R kernel).
Whether a workspace is configured, and any tracked documents needing attention.
Anything that looks broken, with the exact command that revealed it.

---name: doctordescription: Check the health of the Stencila CLI installation - version, available upgrades, kernels, linters, external tools, and workspace configuration. The first thing to run when anything Stencila-related is not working.---# /stencila:doctorDiagnose the Stencila installation and workspace. Report findings as a shortsummary, not raw command output.## 1. Resolve the CLIUse the first of these that exists (the same ladder the plugin'sSessionStart hook uses — if session context already reports a resolved path,use that and skip to step 2):1. The path in the plugin's `stencila_path` setting: `${CLAUDE_PLUGIN_OPTION_STENCILA_PATH}` (if set and not the default `stencila`)2. `./target/debug/stencila` (when working in the Stencila source repo)3. `stencila` on PATH (`command -v stencila`)4. `/usr/local/bin/stencila`, `~/.local/bin/stencila`, `~/.cargo/bin/stencila`**If no CLI is found**: report that Stencila is not installed and give theplatform-appropriate install command —- macOS / Linux: `curl -LsSf https://stencila.io/install.sh | bash`- Windows: download the ZIP for the latest release from <https://github.com/stencila/stencila/releases>Offer to run the installer, but **never run it unprompted** — wait for theuser to say yes. Then stop; the remaining checks need a CLI.## 2. Run the checksWith `<stencila>` as the resolved path, run (all with `NO_COLOR=1` and`--yes`):```shNO_COLOR=1 <stencila> --version --yes # version (plugin tested against 2.14)NO_COLOR=1 <stencila> upgrade --check --yes # available upgrade (does NOT install)NO_COLOR=1 <stencila> kernels list --yes # execution kernels and availabilityNO_COLOR=1 <stencila> linters list --yes # lintersNO_COLOR=1 <stencila> tools list --yes # external tools (pandoc, chrome, etc.)```Also check the workspace: does `stencila.toml` (or `stencila.local.toml`)exist in this or an ancestor directory? If yes, run`NO_COLOR=1 <stencila> status --no-remotes --yes` for tracked-documentstatus.## 3. ReportSummarise in a few lines:- Resolved CLI path and version; warn (do not fail) if the version is below 2.14, and mention `stencila upgrade` if an upgrade is available — do not run it without being asked.- Kernels relevant to the user's documents that are unavailable (e.g. R documents but no R kernel).- Whether a workspace is configured, and any tracked documents needing attention.- Anything that looks broken, with the exact command that revealed it.

Frequently asked questions

Doctor