platform/plugin-development/command-development/SKILL.md
This skill should be used when the user asks to "create a slash command", "add a command", "write a custom command", "define command arguments", "use command frontmatter", "organize commands", "create command with file references", "interactive command", "use AskUserQuestion in command", or needs guidance on slash command structure, YAML frontmatter fields, dynamic arguments, bash execution in commands, user interaction patterns, or command development best practices for Claude Code.
npx skillsauth add harsh040506/claude-code-unified-skill-plugin-library command-developmentInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Slash commands are frequently-used prompts defined as Markdown files that Claude executes during interactive sessions. Understanding command structure, frontmatter options, and dynamic features enables creating powerful, reusable workflows.
Key concepts:
A slash command is a Markdown file containing a prompt that Claude executes when invoked. Commands provide:
Commands are written for agent consumption, not human consumption.
When a user invokes /command-name, the command content is injected into Claude's context as an instruction set — not as a chat message from the user. Claude reads it as its own directive, processes it, and executes. This means the audience of every line in a command file is Claude's planning process, not a human reader.
This distinction matters because the two audiences require fundamentally different language:
When you write user-facing prose in a command, Claude receives an explanation of what should happen rather than a directive for what to do. It often follows politely anyway, but the ambiguity creates inconsistent behavior — especially when the prose has conditionals, passive voice, or future tense.
Correct approach (instructions for Claude):
Review this code for security vulnerabilities including:
- SQL injection
- XSS attacks
- Authentication issues
Provide specific line numbers and severity ratings.
Incorrect approach (messages to user):
This command will review your code for security issues.
You'll receive a report with vulnerability details.
Common hybrid mistake (looks like instructions but is framed for the user):
When you run this command, Claude will look for SQL injection, XSS,
and authentication vulnerabilities in your code. The report you receive
will include line numbers and severity ratings for each issue found.
This fails because "when you run this command" and "the report you receive" address the user, not Claude. The passive construction ("will be included") doesn't commit Claude to an action. Reframe every sentence as a direct directive: "Analyze the code for SQL injection, XSS, and authentication vulnerabilities. Report each finding with its line number and severity rating."
Project commands (shared with team):
.claude/commands//helpPersonal commands (available everywhere):
~/.claude/commands//helpPlugin commands (bundled with plugins):
plugin-name/commands//helpCommands are Markdown files with .md extension:
.claude/commands/
├── review.md # /review command
├── test.md # /test command
└── deploy.md # /deploy command
Simple command:
Review this code for security vulnerabilities including:
- SQL injection
- XSS attacks
- Authentication bypass
- Insecure data handling
No frontmatter needed for basic commands.
Add configuration using YAML frontmatter:
---
description: Review code for security issues
allowed-tools: Read, Grep, Bash(git:*)
model: sonnet
---
Review this code for security vulnerabilities...
Purpose: Brief description shown in /help
Type: String
Default: First line of command prompt
---
description: Review pull request for code quality
---
Best practice: Clear, actionable description (under 60 characters)
Why this matters: The description is what users see when they type /help or start typing a / command. A vague description like "Code stuff" means users won't know to invoke the command; a command that never gets invoked provides no value regardless of how well it's written. The description also determines discoverability — users often find commands by browsing /help rather than knowing their exact name.
Decision heuristic: Write the description as if answering "What will this do when I run it?" in one sentence. If you need more than one sentence, the command scope is too broad.
Purpose: Specify which tools command can use Type: String or Array Default: Inherits from conversation
---
allowed-tools: Read, Write, Edit, Bash(git:*)
---
Patterns:
Read, Write, Edit - Specific toolsBash(git:*) - Bash with git commands only* - All tools (rarely needed)Use when: Command requires specific tool access
Why this matters: Without allowed-tools, a command inherits whatever the conversation's current tool permissions are — which may be more or less than the command needs. This creates two failure modes: (1) the command tries to use a tool the conversation has disabled and errors out, or (2) the command has broader tool access than intended, creating security surface. Explicitly scoping tools makes the command self-contained and predictable regardless of where it's invoked.
Decision heuristic: Start with the minimum set that makes the command work. Add Bash(git:*) only if the command reads git history or status. Add Write only if it produces output files. Omit the field only for read-only commands where inheriting context permissions is intentional.
Purpose: Specify model for command execution Type: String (sonnet, opus, haiku) Default: Inherits from conversation
---
model: haiku
---
Use cases:
haiku - Fast, simple commandssonnet - Standard workflowsopus - Complex analysisWhy this matters: Model selection directly determines cost, latency, and capability ceiling for every invocation. A formatting command that specifies opus wastes budget on a task that haiku handles equally well. A complex analysis command that defaults to haiku may produce shallow outputs because the model lacks the reasoning depth the task requires. Explicit model selection locks in predictable cost and performance rather than varying with whatever model the user happens to have active.
Decision heuristic:
| Command type | Recommended model |
|--------------|-------------------|
| Formatting, templating, simple transforms | haiku |
| Standard code generation, analysis, multi-step workflows | sonnet (or omit) |
| Deep reasoning, complex design decisions, strategic review | opus |
| Commands where accuracy matters more than speed | opus |
| Commands where latency matters more than depth | haiku |
Purpose: Document expected arguments for autocomplete Type: String Default: None
---
argument-hint: [pr-number] [priority] [assignee]
---
Benefits:
Why this matters: Without an argument-hint, the command appears in /help with no indication of what to type after it. Users either have to read the command source or guess. This is a significant usability gap for commands that take structured arguments like PR numbers, file paths, or flags. The hint acts as an inline signature for the command.
Decision heuristic: Use angle brackets for required args <pr-number>, square brackets for optional ones [priority]. List args in invocation order. Keep it short enough to fit on one line in the /help panel (under 40 characters).
Purpose: Prevent SlashCommand tool from programmatically calling command Type: Boolean Default: false
---
disable-model-invocation: true
---
Use when: Command should only be manually invoked
Capture all arguments as single string:
---
description: Fix issue by number
argument-hint: [issue-number]
---
Fix issue #$ARGUMENTS following our coding standards and best practices.
Usage:
> /fix-issue 123
> /fix-issue 456
Expands to:
Fix issue #123 following our coding standards...
Fix issue #456 following our coding standards...
Capture individual arguments with $1, $2, $3, etc.:
---
description: Review PR with priority and assignee
argument-hint: [pr-number] [priority] [assignee]
---
Review pull request #$1 with priority level $2.
After review, assign to $3 for follow-up.
Usage:
> /review-pr 123 high alice
Expands to:
Review pull request #123 with priority level high.
After review, assign to alice for follow-up.
Mix positional and remaining arguments:
Deploy $1 to $2 environment with options: $3
Usage:
> /deploy api staging --force --skip-tests
Expands to:
Deploy api to staging environment with options: --force --skip-tests
Include file contents in command:
---
description: Review specific file
argument-hint: [file-path]
---
Review @$1 for:
- Code quality
- Best practices
- Potential bugs
Usage:
> /review-file src/api/users.ts
Effect: Claude reads src/api/users.ts before processing command
Reference multiple files:
Compare @src/old-version.js with @src/new-version.js
Identify:
- Breaking changes
- New features
- Bug fixes
Reference known files without arguments:
Review @package.json and @tsconfig.json for consistency
Ensure:
- TypeScript version matches
- Dependencies are aligned
- Build configuration is correct
Commands can execute bash commands inline to dynamically gather context before Claude processes the command. This is useful for including repository state, environment information, or project-specific context.
When to use:
Implementation details:
For complete syntax, examples, and best practices, see references/plugin-features-reference.md section on bash execution. The reference includes the exact syntax and multiple working examples to avoid execution issues
Simple organization for small command sets:
.claude/commands/
├── build.md
├── test.md
├── deploy.md
├── review.md
└── docs.md
Use when: 5-15 commands, no clear categories
Organize commands in subdirectories:
.claude/commands/
├── ci/
│ ├── build.md # /build (project:ci)
│ ├── test.md # /test (project:ci)
│ └── lint.md # /lint (project:ci)
├── git/
│ ├── commit.md # /commit (project:git)
│ └── pr.md # /pr (project:git)
└── docs/
├── generate.md # /generate (project:docs)
└── publish.md # /publish (project:docs)
Benefits:
/helpUse when: 15+ commands, clear categories
/helpallowed-tools when neededargument-hint---
argument-hint: [pr-number]
---
$IF($1,
Review PR #$1,
Please provide a PR number. Usage: /review-pr [number]
)
Bash(git:*) not Bash(*)---
description: Deploy application to environment
argument-hint: [environment] [version]
---
<!--
Usage: /deploy [staging|production] [version]
Requires: AWS credentials configured
Example: /deploy staging v1.2.3
-->
Deploy application to $1 environment using version $2...
---
description: Review code changes
allowed-tools: Read, Bash(git:*)
---
Files changed: !`git diff --name-only`
Review each file for:
1. Code quality and style
2. Potential bugs or issues
3. Test coverage
4. Documentation needs
Provide specific feedback for each file.
---
description: Run tests for specific file
argument-hint: [test-file]
allowed-tools: Bash(npm:*)
---
Run tests: !`npm test $1`
Analyze results and suggest fixes for failures.
---
description: Generate documentation for file
argument-hint: [source-file]
---
Generate comprehensive documentation for @$1 including:
- Function/class descriptions
- Parameter documentation
- Return value descriptions
- Usage examples
- Edge cases and errors
---
description: Complete PR workflow
argument-hint: [pr-number]
allowed-tools: Bash(gh:*), Read
---
PR #$1 Workflow:
1. Fetch PR: !`gh pr view $1`
2. Review changes
3. Run checks
4. Approve or request changes
Command not appearing:
.md extension presentArguments not working:
$1, $2 syntax correctargument-hint matches usageBash execution failing:
allowed-tools includes BashFile references not working:
@ syntax correctPlugin commands have access to ${CLAUDE_PLUGIN_ROOT}, an environment variable that resolves to the plugin's absolute path.
Purpose:
Basic usage:
---
description: Analyze using plugin script
allowed-tools: Bash(node:*)
---
Run analysis: !`node ${CLAUDE_PLUGIN_ROOT}/scripts/analyze.js $1`
Review results and report findings.
Common patterns:
# Execute plugin script
!`bash ${CLAUDE_PLUGIN_ROOT}/scripts/script.sh`
# Load plugin configuration
@${CLAUDE_PLUGIN_ROOT}/config/settings.json
# Use plugin template
@${CLAUDE_PLUGIN_ROOT}/templates/report.md
# Access plugin resources
@${CLAUDE_PLUGIN_ROOT}/docs/reference.md
Why use it:
Plugin commands discovered automatically from commands/ directory:
plugin-name/
├── commands/
│ ├── foo.md # /foo (plugin:plugin-name)
│ ├── bar.md # /bar (plugin:plugin-name)
│ └── utils/
│ └── helper.md # /helper (plugin:plugin-name:utils)
└── plugin.json
Namespace benefits:
/help outputNaming conventions:
Configuration-based pattern:
---
description: Deploy using plugin configuration
argument-hint: [environment]
allowed-tools: Read, Bash(*)
---
Load configuration: @${CLAUDE_PLUGIN_ROOT}/config/$1-deploy.json
Deploy to $1 using configuration settings.
Monitor deployment and report status.
Template-based pattern:
---
description: Generate docs from template
argument-hint: [component]
---
Template: @${CLAUDE_PLUGIN_ROOT}/templates/docs.md
Generate documentation for $1 following template structure.
Multi-script pattern:
---
description: Complete build workflow
allowed-tools: Bash(*)
---
Build: !`bash ${CLAUDE_PLUGIN_ROOT}/scripts/build.sh`
Test: !`bash ${CLAUDE_PLUGIN_ROOT}/scripts/test.sh`
Package: !`bash ${CLAUDE_PLUGIN_ROOT}/scripts/package.sh`
Review outputs and report workflow status.
See references/plugin-features-reference.md for detailed patterns.
Commands can integrate with other plugin components for powerful workflows.
Launch plugin agents for complex tasks:
---
description: Deep code review
argument-hint: [file-path]
---
Initiate comprehensive review of @$1 using the code-reviewer agent.
The agent will analyze:
- Code structure
- Security issues
- Performance
- Best practices
Agent uses plugin resources:
- ${CLAUDE_PLUGIN_ROOT}/config/rules.json
- ${CLAUDE_PLUGIN_ROOT}/checklists/review.md
Key points:
plugin/agents/ directoryLeverage plugin skills for specialized knowledge:
---
description: Document API with standards
argument-hint: [api-file]
---
Document API in @$1 following plugin standards.
Use the api-docs-standards skill to ensure:
- Complete endpoint documentation
- Consistent formatting
- Example quality
- Error documentation
Generate production-ready API docs.
Key points:
plugin/skills/ directoryDesign commands that work with plugin hooks:
See references/plugin-features-reference.md for examples of commands that coordinate with hooks
Combine agents, skills, and scripts:
---
description: Comprehensive review workflow
argument-hint: [file]
allowed-tools: Bash(node:*), Read
---
Target: @$1
Phase 1 - Static Analysis:
!`node ${CLAUDE_PLUGIN_ROOT}/scripts/lint.js $1`
Phase 2 - Deep Review:
Launch code-reviewer agent for detailed analysis.
Phase 3 - Standards Check:
Use coding-standards skill for validation.
Phase 4 - Report:
Template: @${CLAUDE_PLUGIN_ROOT}/templates/review.md
Compile findings into report following template.
When to use:
Commands should validate inputs and resources before processing.
---
description: Deploy with validation
argument-hint: [environment]
---
Validate environment: !`echo "$1" | grep -E "^(dev|staging|prod)$" || echo "INVALID"`
If $1 is valid environment:
Deploy to $1
Otherwise:
Explain valid environments: dev, staging, prod
Show usage: /deploy [environment]
---
description: Process configuration
argument-hint: [config-file]
---
Check file exists: !`test -f $1 && echo "EXISTS" || echo "MISSING"`
If file exists:
Process configuration: @$1
Otherwise:
Explain where to place config file
Show expected format
Provide example configuration
---
description: Run plugin analyzer
allowed-tools: Bash(test:*)
---
Validate plugin setup:
- Script: !`test -x ${CLAUDE_PLUGIN_ROOT}/bin/analyze && echo "✓" || echo "✗"`
- Config: !`test -f ${CLAUDE_PLUGIN_ROOT}/config.json && echo "✓" || echo "✗"`
If all checks pass, run analysis.
Otherwise, report missing components.
---
description: Build with error handling
allowed-tools: Bash(*)
---
Execute build: !`bash ${CLAUDE_PLUGIN_ROOT}/scripts/build.sh 2>&1 || echo "BUILD_FAILED"`
If build succeeded:
Report success and output location
If build failed:
Analyze error output
Suggest likely causes
Provide troubleshooting steps
Best practices:
For detailed frontmatter field specifications, see references/frontmatter-reference.md.
For plugin-specific features and patterns, see references/plugin-features-reference.md.
For command pattern examples, see examples/ directory.
testing
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
tools
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
testing
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.