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

When spec-kit is initialized in a subdirectory that doesn't have its
own .git, but a parent directory does, spec-kit was incorrectly using
the parent's git repository root. This caused specs to be created in
the wrong location.

The fix changes repo root detection to prioritize .specify directory
over git rev-parse, ensuring spec-kit respects its own initialization
boundary rather than inheriting a parent git repo.

Fixes #1932

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: iamaeroplane

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'