fix(scripts): prioritize .specify over git for repo root detection

scripts/bash/common.sh

@@ -1,15 +1,39 @@
 #!/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)}"
+    while [ "$dir" != "/" ]; do
+        if [ -d "$dir/.specify" ]; then
+            echo "$dir"
+            return 0
+        fi
+        dir="$(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
@@ -57,9 +81,11 @@ 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 the .specify root has its own .git directory
 has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
+    local repo_root=$(get_repo_root)
+    [ -d "$repo_root/.git" ]
 }
 
 check_feature_branch() {

scripts/bash/create-new-feature.sh

@@ -162,21 +162,24 @@ 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=$(git rev-parse --show-toplevel)
-    HAS_GIT=true
-else
+REPO_ROOT=$(get_repo_root)
+if [ -z "$REPO_ROOT" ]; then
+    # Fallback to local find_repo_root if common.sh couldn't find it
     REPO_ROOT="$(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
+fi
+
+# Check if git is available at this repo root (not a parent)
+if has_git; then
+    HAS_GIT=true
+else
     HAS_GIT=false
 fi
 

scripts/powershell/common.ps1

@@ -1,7 +1,34 @@
 #!/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)
+
+    $current = $StartDir
+    while ($true) {
+        if (Test-Path (Join-Path $current ".specify")) {
+            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) {
@@ -10,8 +37,8 @@ function Get-RepoRoot {
     } catch {
         # Git command failed
     }
-    
-    # Fall back to script location for non-git repos
+
+    # Final fallback to script location for non-git repos
     return (Resolve-Path (Join-Path $PSScriptRoot "../../..")).Path
 }
 
@@ -58,13 +85,11 @@ function Get-CurrentBranch {
     return "main"
 }
 
+# Check if we have git available at the spec-kit root level
+# Returns true only if the .specify root has its own .git directory
 function Test-HasGit {
-    try {
-        git rev-parse --show-toplevel 2>$null | Out-Null
-        return ($LASTEXITCODE -eq 0)
-    } catch {
-        return $false
-    }
+    $repoRoot = Get-RepoRoot
+    return (Test-Path (Join-Path $repoRoot ".git"))
 }
 
 function Test-FeatureBranch {

scripts/powershell/create-new-feature.ps1

@@ -135,27 +135,23 @@ 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 = $true
-    } else {
-        throw "Git not available"
+# Use common.ps1 functions which prioritize .specify over git
+$repoRoot = Get-RepoRoot
+if (-not $repoRoot) {
+    # Fallback to local Find-RepositoryRoot if common.ps1 couldn't find it
+    $repoRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
+    if (-not $repoRoot) {
+        Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
+        exit 1
     }
-} catch {
-    $repoRoot = $fallbackRoot
-    $hasGit = $false
 }
 
+# Check if git is available at this repo root (not a parent)
+$hasGit = Test-HasGit
+
 Set-Location $repoRoot
 
 $specsDir = Join-Path $repoRoot 'specs'