Upgrade Guide

You have Spec Kit installed and want to upgrade to the latest version to get new features, bug fixes, or updated slash commands. This guide covers both upgrading the CLI tool and updating your project files.

Quick Reference

What to Upgrade Command When to Use
CLI Tool Only uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git Get latest CLI features without touching project files
Project Files specify init --here --force --ai <your-agent> Update slash commands, templates, and scripts in your project
Both Run CLI upgrade, then project update Recommended for major version updates

Part 1: Upgrade the CLI Tool

The CLI tool (specify) is separate from your project files. Upgrade it to get the latest features and bug fixes.

If you installed with uv tool install

uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git

If you use one-shot uvx commands

No upgrade needed—uvx always fetches the latest version. Just run your commands as normal:

uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai copilot

Verify the upgrade

specify check

This shows installed tools and confirms the CLI is working.

Part 2: Updating Project Files

When Spec Kit releases new features (like new slash commands or updated templates), you need to refresh your project's Spec Kit files.

What gets updated?

Running specify init --here --force will update:

  • ✅ Slash command files (.claude/commands/, .github/prompts/, etc.)
  • ✅ Script files (.specify/scripts/)
  • ✅ Template files (.specify/templates/)
  • ✅ Shared memory files (.specify/memory/) - ⚠️ See warnings below

What stays safe?

These files are never touched by the upgrade—the template packages don't even contain them:

  • ✅ Your specifications (specs/001-my-feature/spec.md, etc.) - CONFIRMED SAFE
  • ✅ Your implementation plans (specs/001-my-feature/plan.md, tasks.md, etc.) - CONFIRMED SAFE
  • ✅ Your source code - CONFIRMED SAFE
  • ✅ Your git history - CONFIRMED SAFE

The specs/ directory is completely excluded from template packages and will never be modified during upgrades.

Update command

Run this inside your project directory:

specify init --here --force --ai <your-agent>

Replace <your-agent> with your AI assistant. Refer to this list of Supported AI Agents

Example:

specify init --here --force --ai copilot

Understanding the --force flag

Without --force, the CLI warns you and asks for confirmation:

Warning: Current directory is not empty (25 items)
Template files will be merged with existing content and may overwrite existing files
Proceed? [y/N]

With --force, it skips the confirmation and proceeds immediately.

Important: Your specs/ directory is always safe. The --force flag only affects template files (commands, scripts, templates, memory). Your feature specifications, plans, and tasks in specs/ are never included in upgrade packages and cannot be overwritten.

⚠️ Important Warnings

1. Constitution file will be overwritten

Known issue: specify init --here --force currently overwrites .specify/memory/constitution.md with the default template, erasing any customizations you made.

Workaround:

# 1. Back up your constitution before upgrading
cp .specify/memory/constitution.md .specify/memory/constitution-backup.md

# 2. Run the upgrade
specify init --here --force --ai copilot

# 3. Restore your customized constitution
mv .specify/memory/constitution-backup.md .specify/memory/constitution.md

Or use git to restore it:

# After upgrade, restore from git history
git restore .specify/memory/constitution.md

2. Custom template modifications

If you customized any templates in .specify/templates/, the upgrade will overwrite them. Back them up first:

# Back up custom templates
cp -r .specify/templates .specify/templates-backup

# After upgrade, merge your changes back manually

3. Duplicate slash commands (IDE-based agents)

Some IDE-based agents (like Kilo Code, Windsurf) may show duplicate slash commands after upgrading—both old and new versions appear.

Solution: Manually delete the old command files from your agent's folder.

Example for Kilo Code:

# Navigate to the agent's commands folder
cd .kilocode/rules/

# List files and identify duplicates
ls -la

# Delete old versions (example filenames - yours may differ)
rm speckit.specify-old.md
rm speckit.plan-v1.md

Restart your IDE to refresh the command list.

Common Scenarios

Scenario 1: "I just want new slash commands"

# Upgrade CLI (if using persistent install)
uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git

# Update project files to get new commands
specify init --here --force --ai copilot

# Restore your constitution if customized
git restore .specify/memory/constitution.md

Scenario 2: "I customized templates and constitution"

# 1. Back up customizations
cp .specify/memory/constitution.md /tmp/constitution-backup.md
cp -r .specify/templates /tmp/templates-backup

# 2. Upgrade CLI
uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git

# 3. Update project
specify init --here --force --ai copilot

# 4. Restore customizations
mv /tmp/constitution-backup.md .specify/memory/constitution.md
# Manually merge template changes if needed

Scenario 3: "I see duplicate slash commands in my IDE"

This happens with IDE-based agents (Kilo Code, Windsurf, Roo Code, etc.).

# Find the agent folder (example: .kilocode/rules/)
cd .kilocode/rules/

# List all files
ls -la

# Delete old command files
rm speckit.old-command-name.md

# Restart your IDE

Scenario 4: "I'm working on a project without Git"

If you initialized your project with --no-git, you can still upgrade:

# Manually back up files you customized
cp .specify/memory/constitution.md /tmp/constitution-backup.md

# Run upgrade
specify init --here --force --ai copilot --no-git

# Restore customizations
mv /tmp/constitution-backup.md .specify/memory/constitution.md

The --no-git flag skips git initialization but doesn't affect file updates.

Using --no-git Flag

The --no-git flag tells Spec Kit to skip git repository initialization. This is useful when:

  • You manage version control differently (Mercurial, SVN, etc.)
  • Your project is part of a larger monorepo with existing git setup
  • You're experimenting and don't want version control yet

During initial setup:

specify init my-project --ai copilot --no-git

During upgrade:

specify init --here --force --ai copilot --no-git

What --no-git does NOT do

❌ Does NOT prevent file updates ❌ Does NOT skip slash command installation ❌ Does NOT affect template merging

It only skips running git init and creating the initial commit.

Working without Git

If you use --no-git, you'll need to manage feature directories manually:

Set the SPECIFY_FEATURE environment variable before using planning commands:

# Bash/Zsh
export SPECIFY_FEATURE="001-my-feature"

# PowerShell
$env:SPECIFY_FEATURE = "001-my-feature"

This tells Spec Kit which feature directory to use when creating specs, plans, and tasks.

Why this matters: Without git, Spec Kit can't detect your current branch name to determine the active feature. The environment variable provides that context manually.

Troubleshooting

"Slash commands not showing up after upgrade"

Cause: Agent didn't reload the command files.

Fix:

  1. Restart your IDE/editor completely (not just reload window)
  2. For CLI-based agents, verify files exist: 
    ls -la .claude/commands/      # Claude Code
ls -la .gemini/commands/       # Gemini
ls -la .cursor/commands/       # Cursor
  3. Check agent-specific setup:
    • Codex requires CODEX_HOME environment variable
    • Some agents need workspace restart or cache clearing

"I lost my constitution customizations"

Fix: Restore from git or backup:

# If you committed before upgrading
git restore .specify/memory/constitution.md

# If you backed up manually
cp /tmp/constitution-backup.md .specify/memory/constitution.md

Prevention: Always commit or back up constitution.md before upgrading.

"Warning: Current directory is not empty"

Full warning message:

Warning: Current directory is not empty (25 items)
Template files will be merged with existing content and may overwrite existing files
Do you want to continue? [y/N]

What this means:

This warning appears when you run specify init --here (or specify init .) in a directory that already has files. It's telling you:

  1. The directory has existing content - In the example, 25 files/folders
  2. Files will be merged - New template files will be added alongside your existing files
  3. Some files may be overwritten - If you already have Spec Kit files (.claude/, .specify/, etc.), they'll be replaced with the new versions

What gets overwritten:

Only Spec Kit infrastructure files:

  • Agent command files (.claude/commands/, .github/prompts/, etc.)
  • Scripts in .specify/scripts/
  • Templates in .specify/templates/
  • Memory files in .specify/memory/ (including constitution)

What stays untouched:

  • Your specs/ directory (specifications, plans, tasks)
  • Your source code files
  • Your .git/ directory and git history
  • Any other files not part of Spec Kit templates

How to respond:

  • Type y and press Enter - Proceed with the merge (recommended if upgrading)
  • Type n and press Enter - Cancel the operation
  • Use --force flag - Skip this confirmation entirely: 
    specify init --here --force --ai copilot

When you see this warning:

  • ✅ Expected when upgrading an existing Spec Kit project
  • ✅ Expected when adding Spec Kit to an existing codebase
  • ⚠️ Unexpected if you thought you were creating a new project in an empty directory

Prevention tip: Before upgrading, commit or back up your .specify/memory/constitution.md if you customized it.

"CLI upgrade doesn't seem to work"

Verify the installation:

# Check installed tools
uv tool list

# Should show specify-cli

# Verify path
which specify

# Should point to the uv tool installation directory

If not found, reinstall:

uv tool uninstall specify-cli
uv tool install specify-cli --from git+https://github.com/github/spec-kit.git

"Do I need to run specify every time I open my project?"

Short answer: No, you only run specify init once per project (or when upgrading).

Explanation:

The specify CLI tool is used for:

  • Initial setup: specify init to bootstrap Spec Kit in your project
  • Upgrades: specify init --here --force to update templates and commands
  • Diagnostics: specify check to verify tool installation

Once you've run specify init, the slash commands (like /speckit.specify, /speckit.plan, etc.) are permanently installed in your project's agent folder (.claude/, .github/prompts/, etc.). Your AI assistant reads these command files directly—no need to run specify again.

If your agent isn't recognizing slash commands:

  1. Verify command files exist:

    # For GitHub Copilot
ls -la .github/prompts/

# For Claude
ls -la .claude/commands/

  2. Restart your IDE/editor completely (not just reload window)

  3. Check you're in the correct directory where you ran specify init

  4. For some agents, you may need to reload the workspace or clear cache

Related issue: If Copilot can't open local files or uses PowerShell commands unexpectedly, this is typically an IDE context issue, not related to specify. Try:

  • Restarting VS Code
  • Checking file permissions
  • Ensuring the workspace folder is properly opened

Version Compatibility

Spec Kit follows semantic versioning for major releases. The CLI and project files are designed to be compatible within the same major version.

Best practice: Keep both CLI and project files in sync by upgrading both together during major version changes.

Next Steps

After upgrading:

  • Test new slash commands: Run /speckit.constitution or another command to verify everything works
  • Review release notes: Check GitHub Releases for new features and breaking changes
  • Update workflows: If new commands were added, update your team's development workflows
  • Check documentation: Visit github.io/spec-kit for updated guides
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