fix(changelog): correct 0.4.1 section ordering and version reference (#1954)

* Initial plan

* fix(changelog): correct 0.4.1 section ordering and version reference

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/98bc10bc-f444-4833-bd3a-ab8ea0f5e192

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>

CHANGELOG.md

@@ -1,11 +1,33 @@
 # Changelog
 
-## [0.3.2] - 2026-03-19
+## [0.4.1] - 2026-03-24
 
 ### Changes
 
-- chore: bump version to 0.3.2
-- Add conduct extension to community catalog (#1908)
+- Add checkpoint extension (#1947)
+- fix(scripts): prioritize .specify over git for repo root detection (#1933)
+- docs: add AIDE extension demo to community projects (#1943)
+- fix(templates): add missing Assumptions section to spec template (#1939)
+- chore: bump version to 0.4.1 (#1937)
+
+## [0.4.0] - 2026-03-23
+
+### Changes
+
+- fix(cli): add allow_unicode=True and encoding="utf-8" to YAML I/O (#1936)
+- fix(codex): native skills fallback refresh + legacy prompt suppression (#1930)
+
+- feat(cli): embed core pack in wheel for offline/air-gapped deployment (#1803)
+- ci: increase stale workflow operations-per-run to 250 (#1922)
+- docs: update publishing guide with Category and Effect columns (#1913)
+- fix: Align native skills frontmatter with install_ai_skills (#1920)
+- feat: add timestamp-based branch naming option for `specify init` (#1911)
+- docs: add Extension Comparison Guide for community extensions (#1897)
+- docs: update SUPPORT.md, fix issue templates, add preset submission template (#1910)
+- Add support for Junie (#1831)
+- feat: migrate Codex/agy init to native skills workflow (#1906)
+- chore: bump version to 0.3.2 (#1909)
+
 - feat(extensions): add verify-tasks extension to community catalog (#1871)
 - feat(presets): add enable/disable toggle and update semantics (#1891)
 - feat: add iFlow CLI support (#1875)
@@ -21,6 +43,13 @@
 - Feature/spec kit add pi coding agent pullrequest (#1853)
 - feat: register spec-kit-learn extension (#1883)
 
+## [0.3.2] - 2026-03-19
+
+### Changes
+
+- chore: bump version to 0.3.2
+- Add conduct extension to community catalog (#1908)
+
 ## [0.3.1] - 2026-03-17
 
 ### Changed

README.md

@@ -171,6 +171,8 @@ See Spec-Driven Development in action across different scenarios with these comm
 
 - **[Greenfield Spring Boot MVC with a custom preset](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo)** — Builds a Spring Boot MVC application from scratch using a custom pirate-speak preset, demonstrating how presets can reshape the entire spec-kit experience: specifications become "Voyage Manifests," plans become "Battle Plans," and tasks become "Crew Assignments" — all generated in full pirate vernacular without changing any tooling.
 
+- **[Greenfield Spring Boot + React with a custom extension](https://github.com/mnriem/spec-kit-aide-extension-demo)** — Walks through the **AIDE extension**, a community extension that adds an alternative spec-driven workflow to spec-kit with high-level specs (vision) and low-level specs (work items) organized in a 7-step iterative lifecycle: vision → roadmap → progress tracking → work queue → work items → execution → feedback loops. Uses a family trading platform (Spring Boot 4, React 19, PostgreSQL, Docker Compose) as the scenario to illustrate how the extension mechanism lets you plug in a different style of spec-driven development without changing any core tooling — truly utilizing the "Kit" in Spec Kit.
+
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |

extensions/README.md

@@ -78,6 +78,7 @@ The following community-contributed extensions are available in [`catalog.commun
 |-----------|---------|----------|--------|-----|
 | Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
 | Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
+| Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
 | Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
 | Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
 | Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |

extensions/catalog.community.json

@@ -73,6 +73,35 @@
       "created_at": "2026-03-03T00:00:00Z",
       "updated_at": "2026-03-03T00:00:00Z"
     },
+    "checkpoint": {
+      "name": "Checkpoint Extension",
+      "id": "checkpoint",
+      "description": "An extension to commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end.",
+      "author": "aaronrsun",
+      "version": "1.0.0",
+      "download_url": "https://github.com/aaronrsun/spec-kit-checkpoint/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/aaronrsun/spec-kit-checkpoint",
+      "homepage": "https://github.com/aaronrsun/spec-kit-checkpoint",
+      "documentation": "https://github.com/aaronrsun/spec-kit-checkpoint/blob/main/README.md",
+      "changelog": "https://github.com/aaronrsun/spec-kit-checkpoint/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "checkpoint",
+        "commit"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-22T00:00:00Z",
+      "updated_at": "2026-03-22T00:00:00Z"
+    },
     "cleanup": {
       "name": "Cleanup Extension",
       "id": "cleanup",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.3.2"
+version = "0.4.1"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

scripts/bash/common.sh

@@ -1,15 +1,48 @@
 #!/usr/bin/env bash
 # Common functions and variables for all scripts
 
-# Get repository root, with fallback for non-git repositories
+# Find repository root by searching upward for .specify directory
+# This is the primary marker for spec-kit projects
+find_specify_root() {
+    local dir="${1:-$(pwd)}"
+    # Normalize to absolute path to prevent infinite loop with relative paths
+    # Use -- to handle paths starting with - (e.g., -P, -L)
+    dir="$(cd -- "$dir" 2>/dev/null && pwd)" || return 1
+    local prev_dir=""
+    while true; do
+        if [ -d "$dir/.specify" ]; then
+            echo "$dir"
+            return 0
+        fi
+        # Stop if we've reached filesystem root or dirname stops changing
+        if [ "$dir" = "/" ] || [ "$dir" = "$prev_dir" ]; then
+            break
+        fi
+        prev_dir="$dir"
+        dir="$(dirname "$dir")"
+    done
+    return 1
+}
+
+# Get repository root, prioritizing .specify directory over git
+# This prevents using a parent git repo when spec-kit is initialized in a subdirectory
 get_repo_root() {
+    # First, look for .specify directory (spec-kit's own marker)
+    local specify_root
+    if specify_root=$(find_specify_root); then
+        echo "$specify_root"
+        return
+    fi
+
+    # Fallback to git if no .specify found
     if git rev-parse --show-toplevel >/dev/null 2>&1; then
         git rev-parse --show-toplevel
-    else
-        # Fall back to script location for non-git repos
-        local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-        (cd "$script_dir/../../.." && pwd)
+        return
     fi
+
+    # Final fallback to script location for non-git repos
+    local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+    (cd "$script_dir/../../.." && pwd)
 }
 
 # Get current branch, with fallback for non-git repositories
@@ -20,14 +53,14 @@ get_current_branch() {
         return
     fi
 
-    # Then check git if available
-    if git rev-parse --abbrev-ref HEAD >/dev/null 2>&1; then
-        git rev-parse --abbrev-ref HEAD
+    # Then check git if available at the spec-kit root (not parent)
+    local repo_root=$(get_repo_root)
+    if has_git; then
+        git -C "$repo_root" rev-parse --abbrev-ref HEAD
         return
     fi
 
     # For non-git repos, try to find the latest feature directory
-    local repo_root=$(get_repo_root)
     local specs_dir="$repo_root/specs"
 
     if [[ -d "$specs_dir" ]]; then
@@ -68,9 +101,17 @@ get_current_branch() {
     echo "main"  # Final fallback
 }
 
-# Check if we have git available
+# Check if we have git available at the spec-kit root level
+# Returns true only if git is installed and the repo root is inside a git work tree
+# Handles both regular repos (.git directory) and worktrees/submodules (.git file)
 has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
+    # First check if git command is available (before calling get_repo_root which may use git)
+    command -v git >/dev/null 2>&1 || return 1
+    local repo_root=$(get_repo_root)
+    # Check if .git exists (directory or file for worktrees/submodules)
+    [ -e "$repo_root/.git" ] || return 1
+    # Verify it's actually a valid git work tree
+    git -C "$repo_root" rev-parse --is-inside-work-tree >/dev/null 2>&1
 }
 
 check_feature_branch() {

scripts/bash/create-new-feature.sh

@@ -80,19 +80,6 @@ if [ -z "$FEATURE_DESCRIPTION" ]; then
     exit 1
 fi
 
-# Function to find the repository root by searching for existing project markers
-find_repo_root() {
-    local dir="$1"
-    while [ "$dir" != "/" ]; do
-        if [ -d "$dir/.git" ] || [ -d "$dir/.specify" ]; then
-            echo "$dir"
-            return 0
-        fi
-        dir="$(dirname "$dir")"
-    done
-    return 1
-}
-
 # Function to get highest number from specs directory
 get_highest_from_specs() {
     local specs_dir="$1"
@@ -171,21 +158,16 @@ clean_branch_name() {
     echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }
 
-# Resolve repository root. Prefer git information when available, but fall back
-# to searching for repository markers so the workflow still functions in repositories that
-# were initialised with --no-git.
+# Resolve repository root using common.sh functions which prioritize .specify over git
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
-    REPO_ROOT=$(git rev-parse --show-toplevel)
+REPO_ROOT=$(get_repo_root)
+
+# Check if git is available at this repo root (not a parent)
+if has_git; then
     HAS_GIT=true
 else
-    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
-    if [ -z "$REPO_ROOT" ]; then
-        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
-        exit 1
-    fi
     HAS_GIT=false
 fi
 

scripts/powershell/common.ps1

@@ -1,7 +1,38 @@
 #!/usr/bin/env pwsh
 # Common PowerShell functions analogous to common.sh
 
+# Find repository root by searching upward for .specify directory
+# This is the primary marker for spec-kit projects
+function Find-SpecifyRoot {
+    param([string]$StartDir = (Get-Location).Path)
+
+    # Normalize to absolute path to prevent issues with relative paths
+    # Use -LiteralPath to handle paths with wildcard characters ([, ], *, ?)
+    $current = (Resolve-Path -LiteralPath $StartDir -ErrorAction SilentlyContinue)?.Path
+    if (-not $current) { return $null }
+
+    while ($true) {
+        if (Test-Path -LiteralPath (Join-Path $current ".specify") -PathType Container) {
+            return $current
+        }
+        $parent = Split-Path $current -Parent
+        if ([string]::IsNullOrEmpty($parent) -or $parent -eq $current) {
+            return $null
+        }
+        $current = $parent
+    }
+}
+
+# Get repository root, prioritizing .specify directory over git
+# This prevents using a parent git repo when spec-kit is initialized in a subdirectory
 function Get-RepoRoot {
+    # First, look for .specify directory (spec-kit's own marker)
+    $specifyRoot = Find-SpecifyRoot
+    if ($specifyRoot) {
+        return $specifyRoot
+    }
+
+    # Fallback to git if no .specify found
     try {
         $result = git rev-parse --show-toplevel 2>$null
         if ($LASTEXITCODE -eq 0) {
@@ -10,9 +41,10 @@ function Get-RepoRoot {
     } catch {
         # Git command failed
     }
-    
-    # Fall back to script location for non-git repos
-    return (Resolve-Path (Join-Path $PSScriptRoot "../../..")).Path
+
+    # Final fallback to script location for non-git repos
+    # Use -LiteralPath to handle paths with wildcard characters
+    return (Resolve-Path -LiteralPath (Join-Path $PSScriptRoot "../../..")).Path
 }
 
 function Get-CurrentBranch {
@@ -20,19 +52,21 @@ function Get-CurrentBranch {
     if ($env:SPECIFY_FEATURE) {
         return $env:SPECIFY_FEATURE
     }
-    
-    # Then check git if available
-    try {
-        $result = git rev-parse --abbrev-ref HEAD 2>$null
-        if ($LASTEXITCODE -eq 0) {
-            return $result
-        }
-    } catch {
-        # Git command failed
-    }
-    
-    # For non-git repos, try to find the latest feature directory
+
+    # Then check git if available at the spec-kit root (not parent)
     $repoRoot = Get-RepoRoot
+    if (Test-HasGit) {
+        try {
+            $result = git -C $repoRoot rev-parse --abbrev-ref HEAD 2>$null
+            if ($LASTEXITCODE -eq 0) {
+                return $result
+            }
+        } catch {
+            # Git command failed
+        }
+    }
+
+    # For non-git repos, try to find the latest feature directory
     $specsDir = Join-Path $repoRoot "specs"
     
     if (Test-Path $specsDir) {
@@ -69,9 +103,23 @@ function Get-CurrentBranch {
     return "main"
 }
 
+# Check if we have git available at the spec-kit root level
+# Returns true only if git is installed and the repo root is inside a git work tree
+# Handles both regular repos (.git directory) and worktrees/submodules (.git file)
 function Test-HasGit {
+    # First check if git command is available (before calling Get-RepoRoot which may use git)
+    if (-not (Get-Command git -ErrorAction SilentlyContinue)) {
+        return $false
+    }
+    $repoRoot = Get-RepoRoot
+    # Check if .git exists (directory or file for worktrees/submodules)
+    # Use -LiteralPath to handle paths with wildcard characters
+    if (-not (Test-Path -LiteralPath (Join-Path $repoRoot ".git"))) {
+        return $false
+    }
+    # Verify it's actually a valid git work tree
     try {
-        git rev-parse --show-toplevel 2>$null | Out-Null
+        $null = git -C $repoRoot rev-parse --is-inside-work-tree 2>$null
         return ($LASTEXITCODE -eq 0)
     } catch {
         return $false

scripts/powershell/create-new-feature.ps1

@@ -45,30 +45,6 @@ if ([string]::IsNullOrWhiteSpace($featureDesc)) {
     exit 1
 }
 
-# Resolve repository root. Prefer git information when available, but fall back
-# to searching for repository markers so the workflow still functions in repositories that
-# were initialized with --no-git.
-function Find-RepositoryRoot {
-    param(
-        [string]$StartDir,
-        [string[]]$Markers = @('.git', '.specify')
-    )
-    $current = Resolve-Path $StartDir
-    while ($true) {
-        foreach ($marker in $Markers) {
-            if (Test-Path (Join-Path $current $marker)) {
-                return $current
-            }
-        }
-        $parent = Split-Path $current -Parent
-        if ($parent -eq $current) {
-            # Reached filesystem root without finding markers
-            return $null
-        }
-        $current = $parent
-    }
-}
-
 function Get-HighestNumberFromSpecs {
     param([string]$SpecsDir)
     
@@ -139,26 +115,14 @@ function ConvertTo-CleanBranchName {
     
     return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
 }
-$fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
-if (-not $fallbackRoot) {
-    Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
-    exit 1
-}
-
-# Load common functions (includes Resolve-Template)
+# Load common functions (includes Get-RepoRoot, Test-HasGit, Resolve-Template)
 . "$PSScriptRoot/common.ps1"
 
-try {
-    $repoRoot = git rev-parse --show-toplevel 2>$null
-    if ($LASTEXITCODE -eq 0) {
-        $hasGit = $true
-    } else {
-        throw "Git not available"
-    }
-} catch {
-    $repoRoot = $fallbackRoot
-    $hasGit = $false
-}
+# Use common.ps1 functions which prioritize .specify over git
+$repoRoot = Get-RepoRoot
+
+# Check if git is available at this repo root (not a parent)
+$hasGit = Test-HasGit
 
 Set-Location $repoRoot
 

templates/spec-template.md

@@ -113,3 +113,16 @@
 - **SC-002**: [Measurable metric, e.g., "System handles 1000 concurrent users without degradation"]
 - **SC-003**: [User satisfaction metric, e.g., "90% of users successfully complete primary task on first attempt"]
 - **SC-004**: [Business metric, e.g., "Reduce support tickets related to [X] by 50%"]
+
+## Assumptions
+
+<!--
+  ACTION REQUIRED: The content in this section represents placeholders.
+  Fill them out with the right assumptions based on reasonable defaults
+  chosen when the feature description did not specify certain details.
+-->
+
+- [Assumption about target users, e.g., "Users have stable internet connectivity"]
+- [Assumption about scope boundaries, e.g., "Mobile support is out of scope for v1"]
+- [Assumption about data/environment, e.g., "Existing authentication system will be reused"]
+- [Dependency on existing system/service, e.g., "Requires access to the existing user profile API"]