From 1e794d87e736103bedc737ea6a6090674e3f1af3 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 13:20:39 -0500
Subject: [PATCH 01/13] =?UTF-8?q?feat:=20Git=20extension=20stage=202=20?=
 =?UTF-8?q?=E2=80=94=20GIT=5FBRANCH=5FNAME=20override,=20--force=20for=20e?=
 =?UTF-8?q?xisting=20dirs,=20auto-install=20tests=20(#1940)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Add GIT_BRANCH_NAME env var override to create-new-feature.sh/.ps1
  for exact branch naming (bypasses all prefix/suffix generation)
- Fix --force flag for 'specify init <dir>' into existing directories
- Add TestGitExtensionAutoInstall tests (auto-install, --no-git skip,
  commands registered)
- Add TestFeatureDirectoryResolution tests (env var, feature.json,
  priority, branch fallback)
- Document GIT_BRANCH_NAME in speckit.git.feature.md and specify.md
---
 .../git/commands/speckit.git.feature.md       |  25 ++--
 .../git/scripts/bash/create-new-feature.sh    | 110 +++++++--------
 .../scripts/powershell/create-new-feature.ps1 |  88 ++++++------
 scripts/bash/common.sh                        |  23 +++-
 scripts/powershell/common.ps1                 |  19 ++-
 src/specify_cli/__init__.py                   | 130 ++++--------------
 templates/commands/specify.md                 |  74 ++++++----
 tests/extensions/git/test_git_extension.py    |  22 +--
 tests/integrations/test_cli.py                |  93 +++++++++++++
 tests/test_timestamp_branches.py              | 105 ++++++++++++++
 10 files changed, 421 insertions(+), 268 deletions(-)

diff --git a/extensions/git/commands/speckit.git.feature.md b/extensions/git/commands/speckit.git.feature.md
index 13a7d0784d..1a9c5e35da 100644
--- a/extensions/git/commands/speckit.git.feature.md
+++ b/extensions/git/commands/speckit.git.feature.md
@@ -4,7 +4,7 @@ description: "Create a feature branch with sequential or timestamp numbering"
 
 # Create Feature Branch
 
-Create a new feature branch for the given specification.
+Create and switch to a new git feature branch for the given specification. This command handles **branch creation only** — the spec directory and files are created by the core `/speckit.specify` workflow.
 
 ## User Input
 
@@ -14,10 +14,17 @@ $ARGUMENTS
 
 You **MUST** consider the user input before proceeding (if not empty).
 
+## Environment Variable Override
+
+If the user explicitly provided `GIT_BRANCH_NAME` (e.g., via environment variable, argument, or in their request), pass it through to the script by setting the `GIT_BRANCH_NAME` environment variable before invoking the script. When `GIT_BRANCH_NAME` is set:
+- The script uses the exact value as the branch name, bypassing all prefix/suffix generation
+- `--short-name`, `--number`, and `--timestamp` flags are ignored
+- `FEATURE_NUM` is extracted from the name if it starts with a numeric prefix, otherwise set to the full branch name
+
 ## Prerequisites
 
 - Verify Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, warn the user and skip branch creation (spec directory will still be created)
+- If Git is not available, warn the user and skip branch creation
 
 ## Branch Numbering Mode
 
@@ -45,22 +52,16 @@ Run the appropriate script based on your platform:
 - Do NOT pass `--number` — the script determines the correct next number automatically
 - Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
 - You must only ever run this script once per feature
-- The JSON output will contain BRANCH_NAME and SPEC_FILE paths
-
-If the extension scripts are not found at the `.specify/extensions/git/` path, fall back to:
-- **Bash**: `scripts/bash/create-new-feature.sh`
-- **PowerShell**: `scripts/powershell/create-new-feature.ps1`
+- The JSON output will contain `BRANCH_NAME` and `FEATURE_NUM`
 
 ## Graceful Degradation
 
 If Git is not installed or the current directory is not a Git repository:
-- The script will still create the spec directory under `specs/`
-- A warning will be printed: `[specify] Warning: Git repository not detected; skipped branch creation`
-- The workflow continues normally without branch creation
+- Branch creation is skipped with a warning: `[specify] Warning: Git repository not detected; skipped branch creation`
+- The script still outputs `BRANCH_NAME` and `FEATURE_NUM` so the caller can reference them
 
 ## Output
 
 The script outputs JSON with:
-- `BRANCH_NAME`: The created branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
-- `SPEC_FILE`: Path to the created spec file
+- `BRANCH_NAME`: The branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
 - `FEATURE_NUM`: The numeric or timestamp prefix used
diff --git a/extensions/git/scripts/bash/create-new-feature.sh b/extensions/git/scripts/bash/create-new-feature.sh
index dfae29df73..0e72ce759f 100755
--- a/extensions/git/scripts/bash/create-new-feature.sh
+++ b/extensions/git/scripts/bash/create-new-feature.sh
@@ -71,10 +71,14 @@ while [ $i -le $# ]; do
             echo "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
             echo "  --help, -h          Show this help message"
             echo ""
+            echo "Environment variables:"
+            echo "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
+            echo ""
             echo "Examples:"
             echo "  $0 'Add user authentication system' --short-name 'user-auth'"
             echo "  $0 'Implement OAuth2 integration for API' --number 5"
             echo "  $0 --timestamp --short-name 'user-auth' 'Add user authentication'"
+            echo "  GIT_BRANCH_NAME=my-branch $0 'feature description'"
             exit 0
             ;;
         *)
@@ -258,9 +262,6 @@ fi
 cd "$REPO_ROOT"
 
 SPECS_DIR="$REPO_ROOT/specs"
-if [ "$DRY_RUN" != true ]; then
-    mkdir -p "$SPECS_DIR"
-fi
 
 # Function to generate branch name with stop word filtering
 generate_branch_name() {
@@ -301,40 +302,53 @@ generate_branch_name() {
     fi
 }
 
-# Generate branch name
-if [ -n "$SHORT_NAME" ]; then
-    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
+# Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
+if [ -n "${GIT_BRANCH_NAME:-}" ]; then
+    BRANCH_NAME="$GIT_BRANCH_NAME"
+    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
+    if echo "$BRANCH_NAME" | grep -Eq '^[0-9]+-'; then
+        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]+')
+    elif echo "$BRANCH_NAME" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]{8}-[0-9]{6}')
+    else
+        FEATURE_NUM="$BRANCH_NAME"
+    fi
 else
-    BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
-fi
+    # Generate branch name
+    if [ -n "$SHORT_NAME" ]; then
+        BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
+    else
+        BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
+    fi
 
-# Warn if --number and --timestamp are both specified
-if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
-    >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
-    BRANCH_NUMBER=""
-fi
+    # Warn if --number and --timestamp are both specified
+    if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
+        >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
+        BRANCH_NUMBER=""
+    fi
 
-# Determine branch prefix
-if [ "$USE_TIMESTAMP" = true ]; then
-    FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-else
-    if [ -z "$BRANCH_NUMBER" ]; then
-        if [ "$DRY_RUN" = true ] && [ "$HAS_GIT" = true ]; then
-            BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true)
-        elif [ "$DRY_RUN" = true ]; then
-            HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-            BRANCH_NUMBER=$((HIGHEST + 1))
-        elif [ "$HAS_GIT" = true ]; then
-            BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
-        else
-            HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-            BRANCH_NUMBER=$((HIGHEST + 1))
+    # Determine branch prefix
+    if [ "$USE_TIMESTAMP" = true ]; then
+        FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
+        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+    else
+        if [ -z "$BRANCH_NUMBER" ]; then
+            if [ "$DRY_RUN" = true ] && [ "$HAS_GIT" = true ]; then
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true)
+            elif [ "$DRY_RUN" = true ]; then
+                HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
+                BRANCH_NUMBER=$((HIGHEST + 1))
+            elif [ "$HAS_GIT" = true ]; then
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
+            else
+                HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
+                BRANCH_NUMBER=$((HIGHEST + 1))
+            fi
         fi
-    fi
 
-    FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+        FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
+        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+    fi
 fi
 
 # GitHub enforces a 244-byte limit on branch names
@@ -354,9 +368,6 @@ if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
     >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"
 fi
 
-FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
-SPEC_FILE="$FEATURE_DIR/spec.md"
-
 if [ "$DRY_RUN" != true ]; then
     if [ "$HAS_GIT" = true ]; then
         branch_create_error=""
@@ -391,22 +402,6 @@ if [ "$DRY_RUN" != true ]; then
         >&2 echo "[specify] Warning: Git repository not detected; skipped branch creation for $BRANCH_NAME"
     fi
 
-    mkdir -p "$FEATURE_DIR"
-
-    if [ ! -f "$SPEC_FILE" ]; then
-        if type resolve_template >/dev/null 2>&1; then
-            TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
-        else
-            TEMPLATE=""
-        fi
-        if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
-            cp "$TEMPLATE" "$SPEC_FILE"
-        else
-            echo "Warning: Spec template not found; created empty spec file" >&2
-            touch "$SPEC_FILE"
-        fi
-    fi
-
     printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2
 fi
 
@@ -415,35 +410,30 @@ if $JSON_MODE; then
         if [ "$DRY_RUN" = true ]; then
             jq -cn \
                 --arg branch_name "$BRANCH_NAME" \
-                --arg spec_file "$SPEC_FILE" \
                 --arg feature_num "$FEATURE_NUM" \
-                '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num,DRY_RUN:true}'
+                '{BRANCH_NAME:$branch_name,FEATURE_NUM:$feature_num,DRY_RUN:true}'
         else
             jq -cn \
                 --arg branch_name "$BRANCH_NAME" \
-                --arg spec_file "$SPEC_FILE" \
                 --arg feature_num "$FEATURE_NUM" \
-                '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num}'
+                '{BRANCH_NAME:$branch_name,FEATURE_NUM:$feature_num}'
         fi
     else
         if type json_escape >/dev/null 2>&1; then
             _je_branch=$(json_escape "$BRANCH_NAME")
-            _je_spec=$(json_escape "$SPEC_FILE")
             _je_num=$(json_escape "$FEATURE_NUM")
         else
             _je_branch="$BRANCH_NAME"
-            _je_spec="$SPEC_FILE"
             _je_num="$FEATURE_NUM"
         fi
         if [ "$DRY_RUN" = true ]; then
-            printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s","DRY_RUN":true}\n' "$_je_branch" "$_je_spec" "$_je_num"
+            printf '{"BRANCH_NAME":"%s","FEATURE_NUM":"%s","DRY_RUN":true}\n' "$_je_branch" "$_je_num"
         else
-            printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$_je_branch" "$_je_spec" "$_je_num"
+            printf '{"BRANCH_NAME":"%s","FEATURE_NUM":"%s"}\n' "$_je_branch" "$_je_num"
         fi
     fi
 else
     echo "BRANCH_NAME: $BRANCH_NAME"
-    echo "SPEC_FILE: $SPEC_FILE"
     echo "FEATURE_NUM: $FEATURE_NUM"
     if [ "$DRY_RUN" != true ]; then
         printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
diff --git a/extensions/git/scripts/powershell/create-new-feature.ps1 b/extensions/git/scripts/powershell/create-new-feature.ps1
index 75a4e69814..4bd5246259 100644
--- a/extensions/git/scripts/powershell/create-new-feature.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature.ps1
@@ -29,6 +29,10 @@ if ($Help) {
     Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
     Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
     Write-Host "  -Help               Show this help message"
+    Write-Host ""
+    Write-Host "Environment variables:"
+    Write-Host "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
+    Write-Host ""
     exit 0
 }
 
@@ -216,9 +220,6 @@ if (Get-Command Test-HasGit -ErrorAction SilentlyContinue) {
 Set-Location $repoRoot
 
 $specsDir = Join-Path $repoRoot 'specs'
-if (-not $DryRun) {
-    New-Item -ItemType Directory -Path $specsDir -Force | Out-Null
-}
 
 function Get-BranchName {
     param([string]$Description)
@@ -255,35 +256,48 @@ function Get-BranchName {
     }
 }
 
-if ($ShortName) {
-    $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
+# Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
+if ($env:GIT_BRANCH_NAME) {
+    $branchName = $env:GIT_BRANCH_NAME
+    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
+    if ($branchName -match '^(\d+)-') {
+        $featureNum = $matches[1]
+    } elseif ($branchName -match '^(\d{8}-\d{6})-') {
+        $featureNum = $matches[1]
+    } else {
+        $featureNum = $branchName
+    }
 } else {
-    $branchSuffix = Get-BranchName -Description $featureDesc
-}
+    if ($ShortName) {
+        $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
+    } else {
+        $branchSuffix = Get-BranchName -Description $featureDesc
+    }
 
-if ($Timestamp -and $Number -ne 0) {
-    Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
-    $Number = 0
-}
+    if ($Timestamp -and $Number -ne 0) {
+        Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
+        $Number = 0
+    }
 
-if ($Timestamp) {
-    $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
-    $branchName = "$featureNum-$branchSuffix"
-} else {
-    if ($Number -eq 0) {
-        if ($DryRun -and $hasGit) {
-            $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch
-        } elseif ($DryRun) {
-            $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
-        } elseif ($hasGit) {
-            $Number = Get-NextBranchNumber -SpecsDir $specsDir
-        } else {
-            $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
+    if ($Timestamp) {
+        $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
+        $branchName = "$featureNum-$branchSuffix"
+    } else {
+        if ($Number -eq 0) {
+            if ($DryRun -and $hasGit) {
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch
+            } elseif ($DryRun) {
+                $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
+            } elseif ($hasGit) {
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir
+            } else {
+                $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
+            }
         }
-    }
 
-    $featureNum = ('{0:000}' -f $Number)
-    $branchName = "$featureNum-$branchSuffix"
+        $featureNum = ('{0:000}' -f $Number)
+        $branchName = "$featureNum-$branchSuffix"
+    }
 }
 
 $maxBranchLength = 244
@@ -302,9 +316,6 @@ if ($branchName.Length -gt $maxBranchLength) {
     Write-Warning "[specify] Truncated to: $branchName ($($branchName.Length) bytes)"
 }
 
-$featureDir = Join-Path $specsDir $branchName
-$specFile = Join-Path $featureDir 'spec.md'
-
 if (-not $DryRun) {
     if ($hasGit) {
         $branchCreated = $false
@@ -357,28 +368,12 @@ if (-not $DryRun) {
         }
     }
 
-    New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
-
-    if (-not (Test-Path -PathType Leaf $specFile)) {
-        if (Get-Command Resolve-Template -ErrorAction SilentlyContinue) {
-            $template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
-        } else {
-            $template = $null
-        }
-        if ($template -and (Test-Path $template)) {
-            Copy-Item $template $specFile -Force
-        } else {
-            New-Item -ItemType File -Path $specFile -Force | Out-Null
-        }
-    }
-
     $env:SPECIFY_FEATURE = $branchName
 }
 
 if ($Json) {
     $obj = [PSCustomObject]@{
         BRANCH_NAME = $branchName
-        SPEC_FILE = $specFile
         FEATURE_NUM = $featureNum
         HAS_GIT = $hasGit
     }
@@ -388,7 +383,6 @@ if ($Json) {
     $obj | ConvertTo-Json -Compress
 } else {
     Write-Output "BRANCH_NAME: $branchName"
-    Write-Output "SPEC_FILE: $specFile"
     Write-Output "FEATURE_NUM: $featureNum"
     Write-Output "HAS_GIT: $hasGit"
     if (-not $DryRun) {
diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index 5e45e8708c..c38ed5f44e 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -194,9 +194,28 @@ get_feature_paths() {
         has_git_repo="true"
     fi
 
-    # Use prefix-based lookup to support multiple branches per spec
+    # Resolve feature directory.  Priority:
+    #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
+    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
+    #   3. Branch-name-based prefix lookup (legacy fallback)
     local feature_dir
-    if ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
+    if [[ -n "${SPECIFY_FEATURE_DIRECTORY:-}" ]]; then
+        feature_dir="$SPECIFY_FEATURE_DIRECTORY"
+    elif [[ -f "$repo_root/.specify/feature.json" ]]; then
+        local _fd
+        if command -v jq >/dev/null 2>&1; then
+            _fd=$(jq -r '.feature_directory // empty' "$repo_root/.specify/feature.json" 2>/dev/null)
+        else
+            # Minimal fallback: extract value with grep/sed when jq is unavailable
+            _fd=$(grep -o '"feature_directory"[[:space:]]*:[[:space:]]*"[^"]*"' "$repo_root/.specify/feature.json" 2>/dev/null | sed 's/.*"\([^"]*\)"$/\1/')
+        fi
+        if [[ -n "$_fd" ]]; then
+            feature_dir="$_fd"
+        elif ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
+            echo "ERROR: Failed to resolve feature directory" >&2
+            return 1
+        fi
+    elif ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
         echo "ERROR: Failed to resolve feature directory" >&2
         return 1
     fi
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index 8c8c801ee3..7d4cc670a3 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -160,7 +160,24 @@ function Get-FeaturePathsEnv {
     $repoRoot = Get-RepoRoot
     $currentBranch = Get-CurrentBranch
     $hasGit = Test-HasGit
-    $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
+
+    # Resolve feature directory.  Priority:
+    #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
+    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
+    #   3. Branch-name-based prefix lookup (legacy fallback)
+    $featureJson = Join-Path $repoRoot '.specify/feature.json'
+    if ($env:SPECIFY_FEATURE_DIRECTORY) {
+        $featureDir = $env:SPECIFY_FEATURE_DIRECTORY
+    } elseif (Test-Path $featureJson) {
+        $featureConfig = Get-Content $featureJson -Raw | ConvertFrom-Json
+        if ($featureConfig.feature_directory) {
+            $featureDir = $featureConfig.feature_directory
+        } else {
+            $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
+        }
+    } else {
+        $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
+    }
     
     [PSCustomObject]@{
         REPO_ROOT     = $repoRoot
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 95ab2028c1..609daf7315 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -384,61 +384,6 @@ def check_tool(tool: str, tracker: StepTracker = None) -> bool:
 
     return found
 
-def is_git_repo(path: Path = None) -> bool:
-    """Check if the specified path is inside a git repository."""
-    if path is None:
-        path = Path.cwd()
-
-    if not path.is_dir():
-        return False
-
-    try:
-        # Use git command to check if inside a work tree
-        subprocess.run(
-            ["git", "rev-parse", "--is-inside-work-tree"],
-            check=True,
-            capture_output=True,
-            cwd=path,
-        )
-        return True
-    except (subprocess.CalledProcessError, FileNotFoundError):
-        return False
-
-def init_git_repo(project_path: Path, quiet: bool = False) -> Tuple[bool, Optional[str]]:
-    """Initialize a git repository in the specified path.
-
-    Args:
-        project_path: Path to initialize git repository in
-        quiet: if True suppress console output (tracker handles status)
-
-    Returns:
-        Tuple of (success: bool, error_message: Optional[str])
-    """
-    try:
-        original_cwd = Path.cwd()
-        os.chdir(project_path)
-        if not quiet:
-            console.print("[cyan]Initializing git repository...[/cyan]")
-        subprocess.run(["git", "init"], check=True, capture_output=True, text=True)
-        subprocess.run(["git", "add", "."], check=True, capture_output=True, text=True)
-        subprocess.run(["git", "commit", "-m", "Initial commit from Specify template"], check=True, capture_output=True, text=True)
-        if not quiet:
-            console.print("[green]✓[/green] Git repository initialized")
-        return True, None
-
-    except subprocess.CalledProcessError as e:
-        error_msg = f"Command: {' '.join(e.cmd)}\nExit code: {e.returncode}"
-        if e.stderr:
-            error_msg += f"\nError: {e.stderr.strip()}"
-        elif e.stdout:
-            error_msg += f"\nOutput: {e.stdout.strip()}"
-
-        if not quiet:
-            console.print(f"[red]Error initializing git repository:[/red] {e}")
-        return False, error_msg
-    finally:
-        os.chdir(original_cwd)
-
 def handle_vscode_settings(sub_item, dest_file, rel_path, verbose=False, tracker=None) -> None:
     """Handle merging or copying of .vscode/settings.json files.
 
@@ -1011,16 +956,21 @@ def init(
     else:
         project_path = Path(project_name).resolve()
         if project_path.exists():
-            error_panel = Panel(
-                f"Directory '[cyan]{project_name}[/cyan]' already exists\n"
-                "Please choose a different project name or remove the existing directory.",
-                title="[red]Directory Conflict[/red]",
-                border_style="red",
-                padding=(1, 2)
-            )
-            console.print()
-            console.print(error_panel)
-            raise typer.Exit(1)
+            existing_items = list(project_path.iterdir())
+            if force:
+                console.print(f"[cyan]--force supplied: merging into existing directory '[cyan]{project_name}[/cyan]'[/cyan]")
+            else:
+                error_panel = Panel(
+                    f"Directory '[cyan]{project_name}[/cyan]' already exists\n"
+                    "Please choose a different project name or remove the existing directory.\n"
+                    "Use [bold]--force[/bold] to merge into the existing directory.",
+                    title="[red]Directory Conflict[/red]",
+                    border_style="red",
+                    padding=(1, 2)
+                )
+                console.print()
+                console.print(error_panel)
+                raise typer.Exit(1)
 
     if ai_assistant:
         if ai_assistant not in AGENT_CONFIG:
@@ -1066,11 +1016,7 @@ def init(
 
     console.print(Panel("\n".join(setup_lines), border_style="cyan", padding=(1, 2)))
 
-    should_init_git = False
-    if not no_git:
-        should_init_git = check_tool("git")
-        if not should_init_git:
-            console.print("[yellow]Git not found - will skip repository initialization[/yellow]")
+
 
     if not ignore_agent_tools:
         agent_config = AGENT_CONFIG.get(selected_ai)
@@ -1123,14 +1069,11 @@ def init(
     for key, label in [
         ("chmod", "Ensure scripts executable"),
         ("constitution", "Constitution setup"),
-        ("git", "Initialize git repository"),
+        ("git", "Install git extension"),
         ("final", "Finalize"),
     ]:
         tracker.add(key, label)
 
-    # Track git error message outside Live context so it persists
-    git_error_message = None
-
     with Live(tracker.render(), console=console, refresh_per_second=8, transient=True) as live:
         tracker.attach_refresh(lambda: live.update(tracker.render()))
         try:
@@ -1183,17 +1126,19 @@ def init(
 
             if not no_git:
                 tracker.start("git")
-                if is_git_repo(project_path):
-                    tracker.complete("git", "existing repo detected")
-                elif should_init_git:
-                    success, error_msg = init_git_repo(project_path, quiet=True)
-                    if success:
-                        tracker.complete("git", "initialized")
+                try:
+                    from .extensions import ExtensionManager
+                    bundled_path = _locate_bundled_extension("git")
+                    if bundled_path:
+                        manager = ExtensionManager(project_path)
+                        manager.install_from_directory(
+                            bundled_path, get_speckit_version()
+                        )
+                        tracker.complete("git", "git extension installed")
                     else:
-                        tracker.error("git", "init failed")
-                        git_error_message = error_msg
-                else:
-                    tracker.skip("git", "git not available")
+                        tracker.skip("git", "bundled git extension not found")
+                except Exception as ext_err:
+                    tracker.error("git", f"install failed: {ext_err}")
             else:
                 tracker.skip("git", "--no-git flag")
 
@@ -1271,23 +1216,6 @@ def init(
     console.print(tracker.render())
     console.print("\n[bold green]Project ready.[/bold green]")
 
-    # Show git error details if initialization failed
-    if git_error_message:
-        console.print()
-        git_error_panel = Panel(
-            f"[yellow]Warning:[/yellow] Git repository initialization failed\n\n"
-            f"{git_error_message}\n\n"
-            f"[dim]You can initialize git manually later with:[/dim]\n"
-            f"[cyan]cd {project_path if not here else '.'}[/cyan]\n"
-            f"[cyan]git init[/cyan]\n"
-            f"[cyan]git add .[/cyan]\n"
-            f"[cyan]git commit -m \"Initial commit\"[/cyan]",
-            title="[red]Git Initialization Failed[/red]",
-            border_style="red",
-            padding=(1, 2)
-        )
-        console.print(git_error_panel)
-
     # Agent folder security notice
     agent_config = AGENT_CONFIG.get(selected_ai)
     if agent_config:
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index a81b8f12f1..bd5ca2a108 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -8,9 +8,6 @@ handoffs:
     agent: speckit.clarify
     prompt: Clarify specification requirements
     send: true
-scripts:
-  sh: scripts/bash/create-new-feature.sh "{ARGS}"
-  ps: scripts/powershell/create-new-feature.ps1 "{ARGS}"
 ---
 
 ## User Input
@@ -61,7 +58,7 @@ The text the user typed after `/speckit.specify` in the triggering message **is*
 
 Given that feature description, do this:
 
-1. **Generate a concise short name** (2-4 words) for the branch:
+1. **Generate a concise short name** (2-4 words) for the feature:
    - Analyze the feature description and extract the most meaningful keywords
    - Create a 2-4 word short name that captures the essence of the feature
    - Use action-noun format when possible (e.g., "add-user-auth", "fix-payment-bug")
@@ -73,30 +70,47 @@ Given that feature description, do this:
      - "Create a dashboard for analytics" → "analytics-dashboard"
      - "Fix payment processing timeout bug" → "fix-payment-timeout"
 
-2. **Create the feature branch** by running the script with `--short-name` (and `--json`). In sequential mode, do NOT pass `--number` — the script auto-detects the next available number. In timestamp mode, the script generates a `YYYYMMDD-HHMMSS` prefix automatically:
+2. **Branch creation** (optional, via hook):
 
-   **Branch numbering mode**: Before running the script, check if `.specify/init-options.json` exists and read the `branch_numbering` value.
-   - If `"timestamp"`, add `--timestamp` (Bash) or `-Timestamp` (PowerShell) to the script invocation
-   - If `"sequential"` or absent, do not add any extra flag (default behavior)
+   If a `before_specify` hook ran successfully in the Pre-Execution Checks above, it will have created/switched to a git branch and output JSON containing `BRANCH_NAME` and `FEATURE_NUM`. Note these values for reference, but the branch name does **not** dictate the spec directory name.
 
-   - Bash example: `{SCRIPT} --json --short-name "user-auth" "Add user authentication"`
-   - Bash (timestamp): `{SCRIPT} --json --timestamp --short-name "user-auth" "Add user authentication"`
-   - PowerShell example: `{SCRIPT} -Json -ShortName "user-auth" "Add user authentication"`
-   - PowerShell (timestamp): `{SCRIPT} -Json -Timestamp -ShortName "user-auth" "Add user authentication"`
+   If the user explicitly provided `GIT_BRANCH_NAME`, pass it through to the hook so the branch script uses the exact value as the branch name (bypassing all prefix/suffix generation).
 
-   **IMPORTANT**:
-   - Do NOT pass `--number` — the script determines the correct next number automatically
-   - Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
-   - You must only ever run this script once per feature
-   - The JSON is provided in the terminal as output - always refer to it to get the actual content you're looking for
-   - The JSON output will contain BRANCH_NAME and SPEC_FILE paths
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
+3. **Create the spec feature directory**:
+
+   Two key variables control where specs live:
+   - `SPECIFY_SPEC_DIRECTORY`: the top-level directory for all specs (default: `specs/`)
+   - `SPECIFY_FEATURE_DIRECTORY`: the directory for this specific feature, always a subdirectory of `SPECIFY_SPEC_DIRECTORY`
+
+   **Resolution order for `SPECIFY_FEATURE_DIRECTORY`**:
+   1. If the user explicitly provided `SPECIFY_FEATURE_DIRECTORY` (e.g., via environment variable, argument, or configuration), use it as-is
+   2. Otherwise, auto-generate it:
+      - Check `.specify/init-options.json` for `branch_numbering`
+      - If `"timestamp"`: prefix is `YYYYMMDD-HHMMSS` (current timestamp)
+      - If `"sequential"` or absent: prefix is `NNN` (next available 3-digit number after scanning existing directories in `SPECIFY_SPEC_DIRECTORY`)
+      - Construct the directory name: `<prefix>-<short-name>` (e.g., `003-user-auth` or `20260319-143022-user-auth`)
+      - Set `SPECIFY_FEATURE_DIRECTORY` to `SPECIFY_SPEC_DIRECTORY/<directory-name>`
 
-3. Load `templates/spec-template.md` to understand required sections.
+   **Create the directory and spec file**:
+   - `mkdir -p SPECIFY_FEATURE_DIRECTORY`
+   - Copy `templates/spec-template.md` to `SPECIFY_FEATURE_DIRECTORY/spec.md` as the starting point
+   - Set `SPEC_FILE` to `SPECIFY_FEATURE_DIRECTORY/spec.md`
+   - Persist the resolved path to `.specify/feature.json`:
+     ```json
+     {
+       "feature_directory": "SPECIFY_FEATURE_DIRECTORY"
+     }
+     ```
+     This allows downstream commands (`/speckit.plan`, `/speckit.tasks`, etc.) to locate the feature directory without relying on git branch name conventions.
+
+   **IMPORTANT**:
+   - You must only create one feature per `/speckit.specify` invocation
+   - The spec directory name and the git branch name are independent — they may be the same but that is the user's choice
+   - The spec directory and file are always created by this command, never by the hook
 
-4. Follow this execution flow:
+4. Load `templates/spec-template.md` to understand required sections.
 
-    1. Parse user description from Input
+5. Follow this execution flow:
        If empty: ERROR "No feature description provided"
     2. Extract key concepts from description
        Identify: actors, actions, data, constraints
@@ -120,11 +134,11 @@ Given that feature description, do this:
     7. Identify Key Entities (if data involved)
     8. Return: SUCCESS (spec ready for planning)
 
-5. Write the specification to SPEC_FILE using the template structure, replacing placeholders with concrete details derived from the feature description (arguments) while preserving section order and headings.
+6. Write the specification to SPEC_FILE using the template structure, replacing placeholders with concrete details derived from the feature description (arguments) while preserving section order and headings.
 
-6. **Specification Quality Validation**: After writing the initial spec, validate it against quality criteria:
+7. **Specification Quality Validation**: After writing the initial spec, validate it against quality criteria:
 
-   a. **Create Spec Quality Checklist**: Generate a checklist file at `FEATURE_DIR/checklists/requirements.md` using the checklist template structure with these validation items:
+   a. **Create Spec Quality Checklist**: Generate a checklist file at `SPECIFY_FEATURE_DIRECTORY/checklists/requirements.md` using the checklist template structure with these validation items:
 
       ```markdown
       # Specification Quality Checklist: [FEATURE NAME]
@@ -214,9 +228,13 @@ Given that feature description, do this:
 
    d. **Update Checklist**: After each validation iteration, update the checklist file with current pass/fail status
 
-7. Report completion with branch name, spec file path, checklist results, and readiness for the next phase (`/speckit.clarify` or `/speckit.plan`).
+8. **Report completion** to the user with:
+   - `SPECIFY_FEATURE_DIRECTORY` — the feature directory path
+   - `SPEC_FILE` — the spec file path
+   - Checklist results summary
+   - Readiness for the next phase (`/speckit.clarify` or `/speckit.plan`)
 
-8. **Check for extension hooks**: After reporting completion, check if `.specify/extensions.yml` exists in the project root.
+9. **Check for extension hooks**: After reporting completion, check if `.specify/extensions.yml` exists in the project root.
    - If it exists, read it and look for entries under the `hooks.after_specify` key
    - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
    - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
@@ -245,7 +263,7 @@ Given that feature description, do this:
        ```
    - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
-**NOTE:** The script creates and checks out the new branch and initializes the spec file before writing.
+**NOTE:** Branch creation is handled by the `before_specify` hook (git extension). Spec directory and file creation are always handled by this core command.
 
 ## Quick Guidelines
 
diff --git a/tests/extensions/git/test_git_extension.py b/tests/extensions/git/test_git_extension.py
index 721bd999f2..098caf53b7 100644
--- a/tests/extensions/git/test_git_extension.py
+++ b/tests/extensions/git/test_git_extension.py
@@ -280,7 +280,6 @@ def test_creates_branch_sequential(self, tmp_path: Path):
         assert result.returncode == 0, result.stderr
         data = json.loads(result.stdout)
         assert data["BRANCH_NAME"] == "001-user-auth"
-        assert "SPEC_FILE" in data
         assert data["FEATURE_NUM"] == "001"
 
     def test_creates_branch_timestamp(self, tmp_path: Path):
@@ -294,18 +293,6 @@ def test_creates_branch_timestamp(self, tmp_path: Path):
         data = json.loads(result.stdout)
         assert re.match(r"^\d{8}-\d{6}-feat$", data["BRANCH_NAME"])
 
-    def test_creates_spec_dir(self, tmp_path: Path):
-        """create-new-feature.sh creates specs directory and spec.md."""
-        project = _setup_project(tmp_path)
-        result = _run_bash(
-            "create-new-feature.sh", project,
-            "--json", "--short-name", "test-feat", "Test feature",
-        )
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        spec_file = Path(data["SPEC_FILE"])
-        assert spec_file.exists(), f"spec.md not created at {spec_file}"
-
     def test_increments_from_existing_specs(self, tmp_path: Path):
         """Sequential numbering increments past existing spec directories."""
         project = _setup_project(tmp_path)
@@ -321,7 +308,7 @@ def test_increments_from_existing_specs(self, tmp_path: Path):
         assert data["FEATURE_NUM"] == "003"
 
     def test_no_git_graceful_degradation(self, tmp_path: Path):
-        """create-new-feature.sh works without git (creates spec dir only)."""
+        """create-new-feature.sh works without git (outputs branch name, skips branch creation)."""
         project = _setup_project(tmp_path, git=False)
         result = _run_bash(
             "create-new-feature.sh", project,
@@ -330,8 +317,8 @@ def test_no_git_graceful_degradation(self, tmp_path: Path):
         assert result.returncode == 0, result.stderr
         assert "Warning" in result.stderr
         data = json.loads(result.stdout)
-        spec_file = Path(data["SPEC_FILE"])
-        assert spec_file.exists()
+        assert "BRANCH_NAME" in data
+        assert "FEATURE_NUM" in data
 
     def test_dry_run(self, tmp_path: Path):
         """--dry-run computes branch name without creating anything."""
@@ -382,7 +369,8 @@ def test_no_git_graceful_degradation(self, tmp_path: Path):
         json_line = [l for l in result.stdout.splitlines() if l.strip().startswith("{")]
         assert json_line, f"No JSON in output: {result.stdout}"
         data = json.loads(json_line[-1])
-        assert Path(data["SPEC_FILE"]).exists()
+        assert "BRANCH_NAME" in data
+        assert "FEATURE_NUM" in data
 
 
 # ── auto-commit.sh Tests ─────────────────────────────────────────────────────
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index 945ce6ac62..e82d6f4085 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -3,6 +3,8 @@
 import json
 import os
 
+import yaml
+
 
 class TestInitIntegrationFlag:
     def test_integration_and_ai_mutually_exclusive(self, tmp_path):
@@ -147,3 +149,94 @@ def test_shared_infra_skips_existing_files(self, tmp_path):
         # Other shared files should still be installed
         assert (scripts_dir / "setup-plan.sh").exists()
         assert (templates_dir / "plan-template.md").exists()
+
+
+class TestGitExtensionAutoInstall:
+    """Tests for auto-installation of the git extension during specify init."""
+
+    def test_git_extension_auto_installed(self, tmp_path):
+        """Without --no-git, the git extension is installed during init."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "git-auto"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "claude", "--script", "sh",
+                "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        # Check that the tracker didn't report a git error
+        assert "install failed" not in result.output, f"git extension install failed: {result.output}"
+
+        # Git extension files should be installed
+        ext_dir = project / ".specify" / "extensions" / "git"
+        assert ext_dir.exists(), "git extension directory not installed"
+        assert (ext_dir / "extension.yml").exists()
+        assert (ext_dir / "scripts" / "bash" / "create-new-feature.sh").exists()
+        assert (ext_dir / "scripts" / "bash" / "initialize-repo.sh").exists()
+
+        # Hooks should be registered
+        extensions_yml = project / ".specify" / "extensions.yml"
+        assert extensions_yml.exists(), "extensions.yml not created"
+        hooks_data = yaml.safe_load(extensions_yml.read_text(encoding="utf-8"))
+        assert "hooks" in hooks_data
+        assert "before_specify" in hooks_data["hooks"]
+        assert "before_constitution" in hooks_data["hooks"]
+
+    def test_no_git_skips_extension(self, tmp_path):
+        """With --no-git, the git extension is NOT installed."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "no-git"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "claude", "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        # Git extension should NOT be installed
+        ext_dir = project / ".specify" / "extensions" / "git"
+        assert not ext_dir.exists(), "git extension should not be installed with --no-git"
+
+    def test_git_extension_commands_registered(self, tmp_path):
+        """Git extension commands are registered with the agent during init."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "git-cmds"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "claude", "--script", "sh",
+                "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        # Git extension commands should be registered with the agent
+        claude_skills = project / ".claude" / "skills"
+        git_skills = [f for f in claude_skills.iterdir() if f.name.startswith("speckit-git-")]
+        assert len(git_skills) > 0, "no git extension commands registered"
diff --git a/tests/test_timestamp_branches.py b/tests/test_timestamp_branches.py
index 2c13853119..e692b30ada 100644
--- a/tests/test_timestamp_branches.py
+++ b/tests/test_timestamp_branches.py
@@ -774,3 +774,108 @@ def test_ps_dry_run_json_absent_without_flag(self, ps_git_repo: Path):
         assert result.returncode == 0, result.stderr
         data = json.loads(result.stdout)
         assert "DRY_RUN" not in data, f"DRY_RUN should not be in normal JSON: {data}"
+
+
+# ── Feature Directory Resolution Tests ───────────────────────────────────────
+
+
+class TestFeatureDirectoryResolution:
+    """Tests for SPECIFY_FEATURE_DIRECTORY and .specify/feature.json resolution."""
+
+    def test_env_var_overrides_branch_lookup(self, git_repo: Path):
+        """SPECIFY_FEATURE_DIRECTORY env var takes priority over branch-based lookup."""
+        custom_dir = git_repo / "my-custom-specs" / "my-feature"
+        custom_dir.mkdir(parents=True)
+
+        result = subprocess.run(
+            ["bash", "-c", f'source "{COMMON_SH}" && get_feature_paths'],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+            env={**os.environ, "SPECIFY_FEATURE_DIRECTORY": str(custom_dir)},
+        )
+        assert result.returncode == 0, result.stderr
+        assert str(custom_dir) in result.stdout
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(custom_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in output")
+
+    def test_feature_json_overrides_branch_lookup(self, git_repo: Path):
+        """feature.json feature_directory takes priority over branch-based lookup."""
+        custom_dir = git_repo / "specs" / "custom-feature"
+        custom_dir.mkdir(parents=True)
+
+        feature_json = git_repo / ".specify" / "feature.json"
+        feature_json.write_text(
+            f'{{"feature_directory": "{custom_dir}"}}\n',
+            encoding="utf-8",
+        )
+
+        result = subprocess.run(
+            ["bash", "-c", f'source "{COMMON_SH}" && get_feature_paths'],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+        )
+        assert result.returncode == 0, result.stderr
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(custom_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in output")
+
+    def test_env_var_takes_priority_over_feature_json(self, git_repo: Path):
+        """Env var wins over feature.json."""
+        env_dir = git_repo / "specs" / "env-feature"
+        env_dir.mkdir(parents=True)
+        json_dir = git_repo / "specs" / "json-feature"
+        json_dir.mkdir(parents=True)
+
+        feature_json = git_repo / ".specify" / "feature.json"
+        feature_json.write_text(
+            f'{{"feature_directory": "{json_dir}"}}\n',
+            encoding="utf-8",
+        )
+
+        result = subprocess.run(
+            ["bash", "-c", f'source "{COMMON_SH}" && get_feature_paths'],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+            env={**os.environ, "SPECIFY_FEATURE_DIRECTORY": str(env_dir)},
+        )
+        assert result.returncode == 0, result.stderr
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(env_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in output")
+
+    def test_fallback_to_branch_lookup(self, git_repo: Path):
+        """Without env var or feature.json, falls back to branch-based lookup."""
+        subprocess.run(["git", "checkout", "-q", "-b", "001-test-feat"], cwd=git_repo, check=True)
+        spec_dir = git_repo / "specs" / "001-test-feat"
+        spec_dir.mkdir(parents=True)
+
+        result = subprocess.run(
+            ["bash", "-c", f'source "{COMMON_SH}" && get_feature_paths'],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+        )
+        assert result.returncode == 0, result.stderr
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(spec_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in output")

From bf7bdbe349b7208d85e946f05e7e43730e98f28d Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 13:35:32 -0500
Subject: [PATCH 02/13] fix: remove unused Tuple import (ruff F401)

---
 src/specify_cli/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 609daf7315..dc5bf97f59 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -35,7 +35,7 @@
 import stat
 import yaml
 from pathlib import Path
-from typing import Any, Optional, Tuple
+from typing import Any, Optional
 
 import typer
 from rich.console import Console

From 355b884b3423dddd06f7c7187b00e5297cf8a0b7 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 13:39:57 -0500
Subject: [PATCH 03/13] fix: address Copilot review feedback (#2117)

- Fix timestamp regex ordering: check YYYYMMDD-HHMMSS before generic
  numeric prefix in both bash and PowerShell
- Set BRANCH_SUFFIX in GIT_BRANCH_NAME override path so 244-byte
  truncation logic works correctly
- Add 244-byte length check for GIT_BRANCH_NAME in PowerShell
- Use existing_items for non-empty dir warning with --force
- Skip git extension install if already installed (idempotent --force)
- Wrap PowerShell feature.json parsing in try/catch for malformed JSON
- Fix PS comment: 'prefix lookup' -> 'exact mapping via Get-FeatureDir'
- Remove non-functional SPECIFY_SPEC_DIRECTORY from specify.md template
---
 extensions/git/scripts/bash/create-new-feature.sh  | 10 +++++++---
 .../git/scripts/powershell/create-new-feature.ps1  |  9 +++++++--
 scripts/powershell/common.ps1                      | 14 +++++++++-----
 src/specify_cli/__init__.py                        | 14 ++++++++++----
 templates/commands/specify.md                      | 10 ++++------
 5 files changed, 37 insertions(+), 20 deletions(-)

diff --git a/extensions/git/scripts/bash/create-new-feature.sh b/extensions/git/scripts/bash/create-new-feature.sh
index 0e72ce759f..7015b862a1 100755
--- a/extensions/git/scripts/bash/create-new-feature.sh
+++ b/extensions/git/scripts/bash/create-new-feature.sh
@@ -306,12 +306,16 @@ generate_branch_name() {
 if [ -n "${GIT_BRANCH_NAME:-}" ]; then
     BRANCH_NAME="$GIT_BRANCH_NAME"
     # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
-    if echo "$BRANCH_NAME" | grep -Eq '^[0-9]+-'; then
-        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]+')
-    elif echo "$BRANCH_NAME" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^[0-9]+ pattern
+    if echo "$BRANCH_NAME" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
         FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]{8}-[0-9]{6}')
+        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
+    elif echo "$BRANCH_NAME" | grep -Eq '^[0-9]+-'; then
+        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]+')
+        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
     else
         FEATURE_NUM="$BRANCH_NAME"
+        BRANCH_SUFFIX="$BRANCH_NAME"
     fi
 else
     # Generate branch name
diff --git a/extensions/git/scripts/powershell/create-new-feature.ps1 b/extensions/git/scripts/powershell/create-new-feature.ps1
index 4bd5246259..47f3f494dc 100644
--- a/extensions/git/scripts/powershell/create-new-feature.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature.ps1
@@ -259,10 +259,15 @@ function Get-BranchName {
 # Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
 if ($env:GIT_BRANCH_NAME) {
     $branchName = $env:GIT_BRANCH_NAME
+    # Check 244-byte limit for override names
+    if ($branchName.Length -gt 244) {
+        throw "GIT_BRANCH_NAME must be 244 bytes or fewer. Provided value is $($branchName.Length) characters; please supply a shorter override branch name."
+    }
     # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
-    if ($branchName -match '^(\d+)-') {
+    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^\d+ pattern
+    if ($branchName -match '^(\d{8}-\d{6})-') {
         $featureNum = $matches[1]
-    } elseif ($branchName -match '^(\d{8}-\d{6})-') {
+    } elseif ($branchName -match '^(\d+)-') {
         $featureNum = $matches[1]
     } else {
         $featureNum = $branchName
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index 7d4cc670a3..3d94f6ef87 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -164,15 +164,19 @@ function Get-FeaturePathsEnv {
     # Resolve feature directory.  Priority:
     #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
     #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
-    #   3. Branch-name-based prefix lookup (legacy fallback)
+    #   3. Exact branch-to-directory mapping via Get-FeatureDir (legacy fallback)
     $featureJson = Join-Path $repoRoot '.specify/feature.json'
     if ($env:SPECIFY_FEATURE_DIRECTORY) {
         $featureDir = $env:SPECIFY_FEATURE_DIRECTORY
     } elseif (Test-Path $featureJson) {
-        $featureConfig = Get-Content $featureJson -Raw | ConvertFrom-Json
-        if ($featureConfig.feature_directory) {
-            $featureDir = $featureConfig.feature_directory
-        } else {
+        try {
+            $featureConfig = Get-Content $featureJson -Raw | ConvertFrom-Json
+            if ($featureConfig.feature_directory) {
+                $featureDir = $featureConfig.feature_directory
+            } else {
+                $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
+            }
+        } catch {
             $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
         }
     } else {
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index dc5bf97f59..882d02af2e 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -958,6 +958,9 @@ def init(
         if project_path.exists():
             existing_items = list(project_path.iterdir())
             if force:
+                if existing_items:
+                    console.print(f"[yellow]Warning:[/yellow] Directory '{project_name}' is not empty ({len(existing_items)} items)")
+                    console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
                 console.print(f"[cyan]--force supplied: merging into existing directory '[cyan]{project_name}[/cyan]'[/cyan]")
             else:
                 error_panel = Panel(
@@ -1131,10 +1134,13 @@ def init(
                     bundled_path = _locate_bundled_extension("git")
                     if bundled_path:
                         manager = ExtensionManager(project_path)
-                        manager.install_from_directory(
-                            bundled_path, get_speckit_version()
-                        )
-                        tracker.complete("git", "git extension installed")
+                        if manager.registry.is_installed("git"):
+                            tracker.skip("git", "git extension already installed")
+                        else:
+                            manager.install_from_directory(
+                                bundled_path, get_speckit_version()
+                            )
+                            tracker.complete("git", "git extension installed")
                     else:
                         tracker.skip("git", "bundled git extension not found")
                 except Exception as ext_err:
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index bd5ca2a108..900343df31 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -78,18 +78,16 @@ Given that feature description, do this:
 
 3. **Create the spec feature directory**:
 
-   Two key variables control where specs live:
-   - `SPECIFY_SPEC_DIRECTORY`: the top-level directory for all specs (default: `specs/`)
-   - `SPECIFY_FEATURE_DIRECTORY`: the directory for this specific feature, always a subdirectory of `SPECIFY_SPEC_DIRECTORY`
+   Specs live under the default `specs/` directory unless the user explicitly provides `SPECIFY_FEATURE_DIRECTORY`.
 
    **Resolution order for `SPECIFY_FEATURE_DIRECTORY`**:
    1. If the user explicitly provided `SPECIFY_FEATURE_DIRECTORY` (e.g., via environment variable, argument, or configuration), use it as-is
-   2. Otherwise, auto-generate it:
+   2. Otherwise, auto-generate it under `specs/`:
       - Check `.specify/init-options.json` for `branch_numbering`
       - If `"timestamp"`: prefix is `YYYYMMDD-HHMMSS` (current timestamp)
-      - If `"sequential"` or absent: prefix is `NNN` (next available 3-digit number after scanning existing directories in `SPECIFY_SPEC_DIRECTORY`)
+      - If `"sequential"` or absent: prefix is `NNN` (next available 3-digit number after scanning existing directories in `specs/`)
       - Construct the directory name: `<prefix>-<short-name>` (e.g., `003-user-auth` or `20260319-143022-user-auth`)
-      - Set `SPECIFY_FEATURE_DIRECTORY` to `SPECIFY_SPEC_DIRECTORY/<directory-name>`
+      - Set `SPECIFY_FEATURE_DIRECTORY` to `specs/<directory-name>`
 
    **Create the directory and spec file**:
    - `mkdir -p SPECIFY_FEATURE_DIRECTORY`

From 670f64219508a0bc4926ac830bfe8ed8de3c47b2 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 13:49:13 -0500
Subject: [PATCH 04/13] fix: address second round of Copilot review feedback
 (#2117)

- Guard shutil.rmtree on init failure: skip cleanup when --force merged
  into a pre-existing directory (prevents data loss)
- Bash: error on GIT_BRANCH_NAME >244 bytes instead of broken truncation
- Fix malformed numbered list in specify.md (restore missing step 1)
- Add claude_skills.exists() assert before iterdir() in test
---
 extensions/git/scripts/bash/create-new-feature.sh | 5 ++++-
 src/specify_cli/__init__.py                       | 5 ++++-
 templates/commands/specify.md                     | 1 +
 tests/integrations/test_cli.py                    | 1 +
 4 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/extensions/git/scripts/bash/create-new-feature.sh b/extensions/git/scripts/bash/create-new-feature.sh
index 7015b862a1..5c8168a25b 100755
--- a/extensions/git/scripts/bash/create-new-feature.sh
+++ b/extensions/git/scripts/bash/create-new-feature.sh
@@ -357,7 +357,10 @@ fi
 
 # GitHub enforces a 244-byte limit on branch names
 MAX_BRANCH_LENGTH=244
-if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
+if [ -n "${GIT_BRANCH_NAME:-}" ] && [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
+    >&2 echo "Error: GIT_BRANCH_NAME must be 244 bytes or fewer. Provided value is ${#BRANCH_NAME} bytes."
+    exit 1
+elif [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
     PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
     MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
 
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 882d02af2e..106e0b9d5b 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -938,9 +938,11 @@ def init(
         console.print(f"[red]Error:[/red] Invalid --branch-numbering value '{branch_numbering}'. Choose from: {', '.join(sorted(BRANCH_NUMBERING_CHOICES))}")
         raise typer.Exit(1)
 
+    dir_existed_before = False
     if here:
         project_name = Path.cwd().name
         project_path = Path.cwd()
+        dir_existed_before = True
 
         existing_items = list(project_path.iterdir())
         if existing_items:
@@ -955,6 +957,7 @@ def init(
                     raise typer.Exit(0)
     else:
         project_path = Path(project_name).resolve()
+        dir_existed_before = project_path.exists()
         if project_path.exists():
             existing_items = list(project_path.iterdir())
             if force:
@@ -1213,7 +1216,7 @@ def init(
                 _label_width = max(len(k) for k, _ in _env_pairs)
                 env_lines = [f"{k.ljust(_label_width)} → [bright_black]{v}[/bright_black]" for k, v in _env_pairs]
                 console.print(Panel("\n".join(env_lines), title="Debug Environment", border_style="magenta"))
-            if not here and project_path.exists():
+            if not here and project_path.exists() and not dir_existed_before:
                 shutil.rmtree(project_path)
             raise typer.Exit(1)
         finally:
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index 900343df31..c1be1d0b5b 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -109,6 +109,7 @@ Given that feature description, do this:
 4. Load `templates/spec-template.md` to understand required sections.
 
 5. Follow this execution flow:
+    1. Parse user description from arguments
        If empty: ERROR "No feature description provided"
     2. Extract key concepts from description
        Identify: actors, actions, data, constraints
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index e82d6f4085..e835507d5e 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -238,5 +238,6 @@ def test_git_extension_commands_registered(self, tmp_path):
 
         # Git extension commands should be registered with the agent
         claude_skills = project / ".claude" / "skills"
+        assert claude_skills.exists(), "Claude skills directory was not created"
         git_skills = [f for f in claude_skills.iterdir() if f.name.startswith("speckit-git-")]
         assert len(git_skills) > 0, "no git extension commands registered"

From ee37b5bae45abb734e23e0294ca97905f1f96c6c Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 14:23:27 -0500
Subject: [PATCH 05/13] fix: use UTF-8 byte count for 244-byte branch name
 limit (#2117)

- Bash: use LC_ALL=C wc -c for byte length instead of ${#VAR}
- PowerShell: use [System.Text.Encoding]::UTF8.GetByteCount() instead
  of .Length (UTF-16 code units)
---
 extensions/git/scripts/bash/create-new-feature.sh        | 8 +++++---
 extensions/git/scripts/powershell/create-new-feature.ps1 | 7 ++++---
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/extensions/git/scripts/bash/create-new-feature.sh b/extensions/git/scripts/bash/create-new-feature.sh
index 5c8168a25b..7d7a886b92 100755
--- a/extensions/git/scripts/bash/create-new-feature.sh
+++ b/extensions/git/scripts/bash/create-new-feature.sh
@@ -357,10 +357,12 @@ fi
 
 # GitHub enforces a 244-byte limit on branch names
 MAX_BRANCH_LENGTH=244
-if [ -n "${GIT_BRANCH_NAME:-}" ] && [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
-    >&2 echo "Error: GIT_BRANCH_NAME must be 244 bytes or fewer. Provided value is ${#BRANCH_NAME} bytes."
+_byte_length() { printf '%s' "$1" | LC_ALL=C wc -c | tr -d ' '; }
+BRANCH_BYTE_LEN=$(_byte_length "$BRANCH_NAME")
+if [ -n "${GIT_BRANCH_NAME:-}" ] && [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH ]; then
+    >&2 echo "Error: GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is ${BRANCH_BYTE_LEN} bytes."
     exit 1
-elif [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
+elif [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH ]; then
     PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
     MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
 
diff --git a/extensions/git/scripts/powershell/create-new-feature.ps1 b/extensions/git/scripts/powershell/create-new-feature.ps1
index 47f3f494dc..843cfc59c0 100644
--- a/extensions/git/scripts/powershell/create-new-feature.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature.ps1
@@ -259,9 +259,10 @@ function Get-BranchName {
 # Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
 if ($env:GIT_BRANCH_NAME) {
     $branchName = $env:GIT_BRANCH_NAME
-    # Check 244-byte limit for override names
-    if ($branchName.Length -gt 244) {
-        throw "GIT_BRANCH_NAME must be 244 bytes or fewer. Provided value is $($branchName.Length) characters; please supply a shorter override branch name."
+    # Check 244-byte limit (UTF-8) for override names
+    $branchNameUtf8ByteCount = [System.Text.Encoding]::UTF8.GetByteCount($branchName)
+    if ($branchNameUtf8ByteCount -gt 244) {
+        throw "GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is $branchNameUtf8ByteCount bytes; please supply a shorter override branch name."
     }
     # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
     # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^\d+ pattern

From 49be364afae62cc43c6fd4b02e66faf3a5543ac1 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 14:38:29 -0500
Subject: [PATCH 06/13] fix: address third round of review feedback (#2117)

- Update --dry-run help text in bash and PowerShell (branch name only)
- Fix specify.md JSON example: use concrete path, not literal variable
- Add TestForceExistingDirectory tests (merge + error without --force)
- Add PowerShell Get-FeaturePathsEnv tests (env var + feature.json)
---
 .../git/scripts/bash/create-new-feature.sh    |  2 +-
 .../scripts/powershell/create-new-feature.ps1 |  2 +-
 templates/commands/specify.md                 |  3 +-
 tests/integrations/test_cli.py                | 47 ++++++++++++++++
 tests/test_timestamp_branches.py              | 53 +++++++++++++++++++
 5 files changed, 104 insertions(+), 3 deletions(-)

diff --git a/extensions/git/scripts/bash/create-new-feature.sh b/extensions/git/scripts/bash/create-new-feature.sh
index 7d7a886b92..02cd2ec1b6 100755
--- a/extensions/git/scripts/bash/create-new-feature.sh
+++ b/extensions/git/scripts/bash/create-new-feature.sh
@@ -64,7 +64,7 @@ while [ $i -le $# ]; do
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
-            echo "  --dry-run           Compute branch name and paths without creating branches, directories, or files"
+            echo "  --dry-run           Compute branch name without creating the branch"
             echo "  --allow-existing-branch  Switch to branch if it already exists instead of failing"
             echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
             echo "  --number N          Specify branch number manually (overrides auto-detection)"
diff --git a/extensions/git/scripts/powershell/create-new-feature.ps1 b/extensions/git/scripts/powershell/create-new-feature.ps1
index 843cfc59c0..291607d1bd 100644
--- a/extensions/git/scripts/powershell/create-new-feature.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature.ps1
@@ -23,7 +23,7 @@ if ($Help) {
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
-    Write-Host "  -DryRun             Compute branch name and paths without creating branches, directories, or files"
+    Write-Host "  -DryRun             Compute branch name without creating the branch"
     Write-Host "  -AllowExistingBranch  Switch to branch if it already exists instead of failing"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
     Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index c1be1d0b5b..15c75ec396 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -96,9 +96,10 @@ Given that feature description, do this:
    - Persist the resolved path to `.specify/feature.json`:
      ```json
      {
-       "feature_directory": "SPECIFY_FEATURE_DIRECTORY"
+       "feature_directory": "<resolved feature dir>"
      }
      ```
+     Write the actual resolved directory path value (for example, `specs/003-user-auth`), not the literal string `SPECIFY_FEATURE_DIRECTORY`.
      This allows downstream commands (`/speckit.plan`, `/speckit.tasks`, etc.) to locate the feature directory without relying on git branch name conventions.
 
    **IMPORTANT**:
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index e835507d5e..1e23e35a7d 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -151,6 +151,53 @@ def test_shared_infra_skips_existing_files(self, tmp_path):
         assert (templates_dir / "plan-template.md").exists()
 
 
+class TestForceExistingDirectory:
+    """Tests for --force merging into an existing named directory."""
+
+    def test_force_merges_into_existing_dir(self, tmp_path):
+        """specify init <dir> --force succeeds when the directory already exists."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        target = tmp_path / "existing-proj"
+        target.mkdir()
+        # Place a pre-existing file to verify it survives the merge
+        marker = target / "user-file.txt"
+        marker.write_text("keep me", encoding="utf-8")
+
+        runner = CliRunner()
+        result = runner.invoke(app, [
+            "init", str(target), "--integration", "copilot", "--force",
+            "--no-git", "--script", "sh",
+        ], catch_exceptions=False)
+
+        assert result.exit_code == 0, f"init --force failed: {result.output}"
+
+        # Pre-existing file should survive
+        assert marker.read_text(encoding="utf-8") == "keep me"
+
+        # Spec Kit files should be installed
+        assert (target / ".specify" / "init-options.json").exists()
+        assert (target / ".specify" / "templates" / "spec-template.md").exists()
+
+    def test_without_force_errors_on_existing_dir(self, tmp_path):
+        """specify init <dir> without --force errors when directory exists."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        target = tmp_path / "existing-proj"
+        target.mkdir()
+
+        runner = CliRunner()
+        result = runner.invoke(app, [
+            "init", str(target), "--integration", "copilot",
+            "--no-git", "--script", "sh",
+        ], catch_exceptions=False)
+
+        assert result.exit_code == 1
+        assert "already exists" in result.output
+
+
 class TestGitExtensionAutoInstall:
     """Tests for auto-installation of the git extension during specify init."""
 
diff --git a/tests/test_timestamp_branches.py b/tests/test_timestamp_branches.py
index e692b30ada..2d2ee7c1a8 100644
--- a/tests/test_timestamp_branches.py
+++ b/tests/test_timestamp_branches.py
@@ -879,3 +879,56 @@ def test_fallback_to_branch_lookup(self, git_repo: Path):
                 break
         else:
             pytest.fail("FEATURE_DIR not found in output")
+
+    @pytest.mark.skipif(not _has_pwsh(), reason="pwsh not installed")
+    def test_ps_env_var_overrides_branch_lookup(self, git_repo: Path):
+        """PowerShell: SPECIFY_FEATURE_DIRECTORY env var takes priority."""
+        common_ps = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+        custom_dir = git_repo / "my-custom-specs" / "ps-feature"
+        custom_dir.mkdir(parents=True)
+
+        ps_cmd = f'. "{common_ps}"; $r = Get-FeaturePathsEnv; Write-Output "FEATURE_DIR=$($r.FEATURE_DIR)"'
+        result = subprocess.run(
+            ["pwsh", "-NoProfile", "-Command", ps_cmd],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+            env={**os.environ, "SPECIFY_FEATURE_DIRECTORY": str(custom_dir)},
+        )
+        assert result.returncode == 0, result.stderr
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(custom_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in PowerShell output")
+
+    @pytest.mark.skipif(not _has_pwsh(), reason="pwsh not installed")
+    def test_ps_feature_json_overrides_branch_lookup(self, git_repo: Path):
+        """PowerShell: feature.json takes priority over branch-based lookup."""
+        common_ps = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+        custom_dir = git_repo / "specs" / "ps-json-feature"
+        custom_dir.mkdir(parents=True)
+
+        feature_json = git_repo / ".specify" / "feature.json"
+        feature_json.write_text(
+            f'{{"feature_directory": "{custom_dir}"}}\n',
+            encoding="utf-8",
+        )
+
+        ps_cmd = f'. "{common_ps}"; $r = Get-FeaturePathsEnv; Write-Output "FEATURE_DIR=$($r.FEATURE_DIR)"'
+        result = subprocess.run(
+            ["pwsh", "-NoProfile", "-Command", ps_cmd],
+            cwd=git_repo,
+            capture_output=True,
+            text=True,
+        )
+        assert result.returncode == 0, result.stderr
+        for line in result.stdout.splitlines():
+            if line.startswith("FEATURE_DIR="):
+                val = line.split("=", 1)[1].strip("'\"")
+                assert val == str(custom_dir)
+                break
+        else:
+            pytest.fail("FEATURE_DIR not found in PowerShell output")

From e5a2988e42d17d6085ff349639c6ebf99a8695b5 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 14:51:21 -0500
Subject: [PATCH 07/13] fix: normalize relative paths and fix Test-HasGit
 compat (#2117)

- Bash common.sh: normalize SPECIFY_FEATURE_DIRECTORY and feature.json
  relative paths to absolute under repo root
- PowerShell common.ps1: same normalization using IsPathRooted + Join-Path
- PowerShell create-new-feature.ps1: call Test-HasGit without -RepoRoot
  for compatibility with core common.ps1 (no param) and git-common.ps1
  (optional param with default)
---
 extensions/git/scripts/powershell/create-new-feature.ps1 | 4 +++-
 scripts/bash/common.sh                                   | 4 ++++
 scripts/powershell/common.ps1                            | 8 ++++++++
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/extensions/git/scripts/powershell/create-new-feature.ps1 b/extensions/git/scripts/powershell/create-new-feature.ps1
index 291607d1bd..3e8b29372d 100644
--- a/extensions/git/scripts/powershell/create-new-feature.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature.ps1
@@ -207,7 +207,9 @@ if (Get-Command Get-RepoRoot -ErrorAction SilentlyContinue) {
 
 # Check if git is available
 if (Get-Command Test-HasGit -ErrorAction SilentlyContinue) {
-    $hasGit = Test-HasGit -RepoRoot $repoRoot
+    # Call without parameters for compatibility with core common.ps1 (no -RepoRoot param)
+    # and git-common.ps1 (has -RepoRoot param with default).
+    $hasGit = Test-HasGit
 } else {
     try {
         git -C $repoRoot rev-parse --is-inside-work-tree 2>$null | Out-Null
diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index c38ed5f44e..98681febf6 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -201,6 +201,8 @@ get_feature_paths() {
     local feature_dir
     if [[ -n "${SPECIFY_FEATURE_DIRECTORY:-}" ]]; then
         feature_dir="$SPECIFY_FEATURE_DIRECTORY"
+        # Normalize relative paths to absolute under repo root
+        [[ "$feature_dir" != /* ]] && feature_dir="$repo_root/$feature_dir"
     elif [[ -f "$repo_root/.specify/feature.json" ]]; then
         local _fd
         if command -v jq >/dev/null 2>&1; then
@@ -211,6 +213,8 @@ get_feature_paths() {
         fi
         if [[ -n "$_fd" ]]; then
             feature_dir="$_fd"
+            # Normalize relative paths to absolute under repo root
+            [[ "$feature_dir" != /* ]] && feature_dir="$repo_root/$feature_dir"
         elif ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
             echo "ERROR: Failed to resolve feature directory" >&2
             return 1
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index 3d94f6ef87..35ed884f0f 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -168,11 +168,19 @@ function Get-FeaturePathsEnv {
     $featureJson = Join-Path $repoRoot '.specify/feature.json'
     if ($env:SPECIFY_FEATURE_DIRECTORY) {
         $featureDir = $env:SPECIFY_FEATURE_DIRECTORY
+        # Normalize relative paths to absolute under repo root
+        if (-not [System.IO.Path]::IsPathRooted($featureDir)) {
+            $featureDir = Join-Path $repoRoot $featureDir
+        }
     } elseif (Test-Path $featureJson) {
         try {
             $featureConfig = Get-Content $featureJson -Raw | ConvertFrom-Json
             if ($featureConfig.feature_directory) {
                 $featureDir = $featureConfig.feature_directory
+                # Normalize relative paths to absolute under repo root
+                if (-not [System.IO.Path]::IsPathRooted($featureDir)) {
+                    $featureDir = Join-Path $repoRoot $featureDir
+                }
             } else {
                 $featureDir = Get-FeatureDir -RepoRoot $repoRoot -Branch $currentBranch
             }

From 0dad208579c40b2832cc1fee29e25af08338ce75 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 15:06:51 -0500
Subject: [PATCH 08/13] test: add GIT_BRANCH_NAME automated tests for bash and
 PowerShell (#2117)

- TestGitBranchNameOverrideBash: 5 tests (exact name, sequential prefix,
  timestamp prefix, overlong rejection, dry-run)
- TestGitBranchNameOverridePowerShell: 4 tests (exact name, sequential
  prefix, timestamp prefix, overlong rejection)
- Tests use extension scripts (not core) via new ext_git_repo and
  ext_ps_git_repo fixtures
---
 tests/test_timestamp_branches.py | 160 +++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)

diff --git a/tests/test_timestamp_branches.py b/tests/test_timestamp_branches.py
index 2d2ee7c1a8..6a3aa3a5ef 100644
--- a/tests/test_timestamp_branches.py
+++ b/tests/test_timestamp_branches.py
@@ -4,6 +4,7 @@
 Converted from tests/test_timestamp_branches.sh so they are discovered by `uv run pytest`.
 """
 
+import json
 import os
 import re
 import shutil
@@ -16,6 +17,8 @@
 CREATE_FEATURE = PROJECT_ROOT / "scripts" / "bash" / "create-new-feature.sh"
 CREATE_FEATURE_PS = PROJECT_ROOT / "scripts" / "powershell" / "create-new-feature.ps1"
 COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+EXT_CREATE_FEATURE = PROJECT_ROOT / "extensions" / "git" / "scripts" / "bash" / "create-new-feature.sh"
+EXT_CREATE_FEATURE_PS = PROJECT_ROOT / "extensions" / "git" / "scripts" / "powershell" / "create-new-feature.ps1"
 
 
 @pytest.fixture
@@ -41,6 +44,62 @@ def git_repo(tmp_path: Path) -> Path:
     return tmp_path
 
 
+@pytest.fixture
+def ext_git_repo(tmp_path: Path) -> Path:
+    """Create a temp git repo with extension scripts (for GIT_BRANCH_NAME tests)."""
+    subprocess.run(["git", "init", "-q"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "config", "user.email", "test@example.com"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=tmp_path, check=True)
+    # Extension script needs common.sh at .specify/scripts/bash/
+    specify_scripts = tmp_path / ".specify" / "scripts" / "bash"
+    specify_scripts.mkdir(parents=True)
+    shutil.copy(COMMON_SH, specify_scripts / "common.sh")
+    # Also install core scripts for compatibility
+    core_scripts = tmp_path / "scripts" / "bash"
+    core_scripts.mkdir(parents=True)
+    shutil.copy(COMMON_SH, core_scripts / "common.sh")
+    # Copy extension script
+    ext_dir = tmp_path / ".specify" / "extensions" / "git" / "scripts" / "bash"
+    ext_dir.mkdir(parents=True)
+    shutil.copy(EXT_CREATE_FEATURE, ext_dir / "create-new-feature.sh")
+    # Also copy git-common.sh if it exists
+    git_common = PROJECT_ROOT / "extensions" / "git" / "scripts" / "bash" / "git-common.sh"
+    if git_common.exists():
+        shutil.copy(git_common, ext_dir / "git-common.sh")
+    (tmp_path / ".specify" / "templates").mkdir(parents=True, exist_ok=True)
+    (tmp_path / "specs").mkdir(exist_ok=True)
+    return tmp_path
+
+
+@pytest.fixture
+def ext_ps_git_repo(tmp_path: Path) -> Path:
+    """Create a temp git repo with PowerShell extension scripts."""
+    subprocess.run(["git", "init", "-q"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "config", "user.email", "test@example.com"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=tmp_path, check=True)
+    subprocess.run(["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=tmp_path, check=True)
+    # Install core PS scripts
+    ps_dir = tmp_path / "scripts" / "powershell"
+    ps_dir.mkdir(parents=True)
+    common_ps = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+    shutil.copy(common_ps, ps_dir / "common.ps1")
+    # Also install at .specify/scripts/powershell/ for extension resolution
+    specify_ps = tmp_path / ".specify" / "scripts" / "powershell"
+    specify_ps.mkdir(parents=True)
+    shutil.copy(common_ps, specify_ps / "common.ps1")
+    # Copy extension script
+    ext_ps = tmp_path / ".specify" / "extensions" / "git" / "scripts" / "powershell"
+    ext_ps.mkdir(parents=True)
+    shutil.copy(EXT_CREATE_FEATURE_PS, ext_ps / "create-new-feature.ps1")
+    git_common_ps = PROJECT_ROOT / "extensions" / "git" / "scripts" / "powershell" / "git-common.ps1"
+    if git_common_ps.exists():
+        shutil.copy(git_common_ps, ext_ps / "git-common.ps1")
+    (tmp_path / ".specify" / "templates").mkdir(parents=True, exist_ok=True)
+    (tmp_path / "specs").mkdir(exist_ok=True)
+    return tmp_path
+
+
 @pytest.fixture
 def no_git_dir(tmp_path: Path) -> Path:
     """Create a temp directory without git, but with scripts."""
@@ -776,6 +835,107 @@ def test_ps_dry_run_json_absent_without_flag(self, ps_git_repo: Path):
         assert "DRY_RUN" not in data, f"DRY_RUN should not be in normal JSON: {data}"
 
 
+# ── GIT_BRANCH_NAME Override Tests ──────────────────────────────────────────
+
+
+class TestGitBranchNameOverrideBash:
+    """Tests for GIT_BRANCH_NAME env var override in extension create-new-feature.sh."""
+
+    def _run_ext(self, ext_git_repo: Path, env_extras: dict, *extra_args: str):
+        script = ext_git_repo / ".specify" / "extensions" / "git" / "scripts" / "bash" / "create-new-feature.sh"
+        cmd = ["bash", str(script), "--json", *extra_args, "ignored"]
+        return subprocess.run(cmd, cwd=ext_git_repo, capture_output=True, text=True,
+                              env={**os.environ, **env_extras})
+
+    def test_exact_name_no_prefix(self, ext_git_repo: Path):
+        """GIT_BRANCH_NAME is used verbatim with no numeric prefix added."""
+        result = self._run_ext(ext_git_repo, {"GIT_BRANCH_NAME": "my-exact-branch"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "my-exact-branch"
+        assert data["FEATURE_NUM"] == "my-exact-branch"
+
+    def test_sequential_prefix_extraction(self, ext_git_repo: Path):
+        """FEATURE_NUM extracted from sequential-style prefix (digits before dash)."""
+        result = self._run_ext(ext_git_repo, {"GIT_BRANCH_NAME": "042-custom-branch"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "042-custom-branch"
+        assert data["FEATURE_NUM"] == "042"
+
+    def test_timestamp_prefix_extraction(self, ext_git_repo: Path):
+        """FEATURE_NUM extracted as full YYYYMMDD-HHMMSS for timestamp-style names."""
+        result = self._run_ext(ext_git_repo, {"GIT_BRANCH_NAME": "20260407-143022-my-feature"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "20260407-143022-my-feature"
+        assert data["FEATURE_NUM"] == "20260407-143022"
+
+    def test_overlong_name_rejected(self, ext_git_repo: Path):
+        """GIT_BRANCH_NAME exceeding 244 bytes is rejected with an error."""
+        long_name = "a" * 245
+        result = self._run_ext(ext_git_repo, {"GIT_BRANCH_NAME": long_name})
+        assert result.returncode != 0
+        assert "244" in result.stderr
+
+    def test_dry_run_with_override(self, ext_git_repo: Path):
+        """GIT_BRANCH_NAME works with --dry-run (no branch created)."""
+        result = self._run_ext(ext_git_repo, {"GIT_BRANCH_NAME": "dry-run-override"}, "--dry-run")
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "dry-run-override"
+        assert data.get("DRY_RUN") is True
+        branches = subprocess.run(
+            ["git", "branch", "--list", "dry-run-override"],
+            cwd=ext_git_repo, capture_output=True, text=True,
+        )
+        assert "dry-run-override" not in branches.stdout
+
+
+@pytest.mark.skipif(not _has_pwsh(), reason="pwsh not installed")
+class TestGitBranchNameOverridePowerShell:
+    """Tests for GIT_BRANCH_NAME env var override in extension create-new-feature.ps1."""
+
+    def _run_ext(self, ext_ps_git_repo: Path, env_extras: dict):
+        script = ext_ps_git_repo / ".specify" / "extensions" / "git" / "scripts" / "powershell" / "create-new-feature.ps1"
+        return subprocess.run(
+            ["pwsh", "-NoProfile", "-File", str(script), "-Json", "ignored"],
+            cwd=ext_ps_git_repo, capture_output=True, text=True,
+            env={**os.environ, **env_extras},
+        )
+
+    def test_exact_name_no_prefix(self, ext_ps_git_repo: Path):
+        """GIT_BRANCH_NAME is used verbatim with no numeric prefix added."""
+        result = self._run_ext(ext_ps_git_repo, {"GIT_BRANCH_NAME": "ps-exact-branch"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "ps-exact-branch"
+        assert data["FEATURE_NUM"] == "ps-exact-branch"
+
+    def test_sequential_prefix_extraction(self, ext_ps_git_repo: Path):
+        """FEATURE_NUM extracted from sequential-style prefix."""
+        result = self._run_ext(ext_ps_git_repo, {"GIT_BRANCH_NAME": "099-ps-numbered"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "099-ps-numbered"
+        assert data["FEATURE_NUM"] == "099"
+
+    def test_timestamp_prefix_extraction(self, ext_ps_git_repo: Path):
+        """FEATURE_NUM extracted as full YYYYMMDD-HHMMSS for timestamp-style names."""
+        result = self._run_ext(ext_ps_git_repo, {"GIT_BRANCH_NAME": "20260407-143022-ps-feature"})
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "20260407-143022-ps-feature"
+        assert data["FEATURE_NUM"] == "20260407-143022"
+
+    def test_overlong_name_rejected(self, ext_ps_git_repo: Path):
+        """GIT_BRANCH_NAME exceeding 244 bytes is rejected."""
+        long_name = "a" * 245
+        result = self._run_ext(ext_ps_git_repo, {"GIT_BRANCH_NAME": long_name})
+        assert result.returncode != 0
+        assert "244" in result.stderr
+
+
 # ── Feature Directory Resolution Tests ───────────────────────────────────────
 
 

From 358eef5148ee39a88299f05dd52194651df9eecf Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 15:39:26 -0500
Subject: [PATCH 09/13] fix: restore git init during specify init + review
 fixes (#2117)

- Restore is_git_repo() and init_git_repo() functions removed in stage 2
- specify init now runs git init AND installs git extension (not just
  extension install alone)
- Add is_dir() guard for non-here path to prevent uncontrolled error
  when target exists but is a file
- Add python3 JSON fallback in common.sh for multi-line feature.json
  (grep pipeline fails on pretty-printed JSON without jq)
---
 scripts/bash/common.sh      |  5 ++-
 src/specify_cli/__init__.py | 78 ++++++++++++++++++++++++++++++++++---
 2 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index 98681febf6..04af7d794f 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -207,8 +207,11 @@ get_feature_paths() {
         local _fd
         if command -v jq >/dev/null 2>&1; then
             _fd=$(jq -r '.feature_directory // empty' "$repo_root/.specify/feature.json" 2>/dev/null)
+        elif command -v python3 >/dev/null 2>&1; then
+            # Fallback: use Python to parse JSON so pretty-printed/multi-line files work
+            _fd=$(python3 -c "import json,sys; d=json.load(open(sys.argv[1])); print(d.get('feature_directory',''))" "$repo_root/.specify/feature.json" 2>/dev/null)
         else
-            # Minimal fallback: extract value with grep/sed when jq is unavailable
+            # Last resort: single-line grep fallback (won't work on multi-line JSON)
             _fd=$(grep -o '"feature_directory"[[:space:]]*:[[:space:]]*"[^"]*"' "$repo_root/.specify/feature.json" 2>/dev/null | sed 's/.*"\([^"]*\)"$/\1/')
         fi
         if [[ -n "$_fd" ]]; then
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 106e0b9d5b..76163ea542 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -384,6 +384,53 @@ def check_tool(tool: str, tracker: StepTracker = None) -> bool:
 
     return found
 
+
+def is_git_repo(path: Path = None) -> bool:
+    """Check if the specified path is inside a git repository."""
+    if path is None:
+        path = Path.cwd()
+
+    if not path.is_dir():
+        return False
+
+    try:
+        subprocess.run(
+            ["git", "rev-parse", "--is-inside-work-tree"],
+            check=True,
+            capture_output=True,
+            cwd=path,
+        )
+        return True
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        return False
+
+
+def init_git_repo(project_path: Path, quiet: bool = False) -> tuple[bool, Optional[str]]:
+    """Initialize a git repository in the specified path."""
+    try:
+        original_cwd = Path.cwd()
+        os.chdir(project_path)
+        if not quiet:
+            console.print("[cyan]Initializing git repository...[/cyan]")
+        subprocess.run(["git", "init"], check=True, capture_output=True, text=True)
+        subprocess.run(["git", "add", "."], check=True, capture_output=True, text=True)
+        subprocess.run(["git", "commit", "-m", "Initial commit from Specify template"], check=True, capture_output=True, text=True)
+        if not quiet:
+            console.print("[green]✓[/green] Git repository initialized")
+        return True, None
+    except subprocess.CalledProcessError as e:
+        error_msg = f"Command: {' '.join(e.cmd)}\nExit code: {e.returncode}"
+        if e.stderr:
+            error_msg += f"\nError: {e.stderr.strip()}"
+        elif e.stdout:
+            error_msg += f"\nOutput: {e.stdout.strip()}"
+        if not quiet:
+            console.print(f"[red]Error initializing git repository:[/red] {e}")
+        return False, error_msg
+    finally:
+        os.chdir(original_cwd)
+
+
 def handle_vscode_settings(sub_item, dest_file, rel_path, verbose=False, tracker=None) -> None:
     """Handle merging or copying of .vscode/settings.json files.
 
@@ -959,6 +1006,9 @@ def init(
         project_path = Path(project_name).resolve()
         dir_existed_before = project_path.exists()
         if project_path.exists():
+            if not project_path.is_dir():
+                console.print(f"[red]Error:[/red] '{project_name}' exists but is not a directory.")
+                raise typer.Exit(1)
             existing_items = list(project_path.iterdir())
             if force:
                 if existing_items:
@@ -1022,7 +1072,11 @@ def init(
 
     console.print(Panel("\n".join(setup_lines), border_style="cyan", padding=(1, 2)))
 
-
+    should_init_git = False
+    if not no_git:
+        should_init_git = check_tool("git")
+        if not should_init_git:
+            console.print("[yellow]Git not found - will skip repository initialization[/yellow]")
 
     if not ignore_agent_tools:
         agent_config = AGENT_CONFIG.get(selected_ai)
@@ -1132,22 +1186,36 @@ def init(
 
             if not no_git:
                 tracker.start("git")
+                git_messages = []
+                # Step 1: Initialize git repo if needed
+                if is_git_repo(project_path):
+                    git_messages.append("existing repo detected")
+                elif should_init_git:
+                    success, error_msg = init_git_repo(project_path, quiet=True)
+                    if success:
+                        git_messages.append("initialized")
+                    else:
+                        git_messages.append("init failed")
+                else:
+                    git_messages.append("git not available")
+                # Step 2: Install bundled git extension
                 try:
                     from .extensions import ExtensionManager
                     bundled_path = _locate_bundled_extension("git")
                     if bundled_path:
                         manager = ExtensionManager(project_path)
                         if manager.registry.is_installed("git"):
-                            tracker.skip("git", "git extension already installed")
+                            git_messages.append("extension already installed")
                         else:
                             manager.install_from_directory(
                                 bundled_path, get_speckit_version()
                             )
-                            tracker.complete("git", "git extension installed")
+                            git_messages.append("extension installed")
                     else:
-                        tracker.skip("git", "bundled git extension not found")
+                        git_messages.append("bundled extension not found")
                 except Exception as ext_err:
-                    tracker.error("git", f"install failed: {ext_err}")
+                    git_messages.append(f"extension install failed: {ext_err}")
+                tracker.complete("git", "; ".join(git_messages))
             else:
                 tracker.skip("git", "--no-git flag")
 

From 11d49196cb5f1f18e48db58ed72c1fdf5969793b Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 15:55:09 -0500
Subject: [PATCH 10/13] fix: use init_git_repo error_msg in failure output
 (#2117)

---
 src/specify_cli/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 76163ea542..e2d8926848 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1195,7 +1195,10 @@ def init(
                     if success:
                         git_messages.append("initialized")
                     else:
-                        git_messages.append("init failed")
+                        if error_msg:
+                            git_messages.append(f"init failed: {error_msg}")
+                        else:
+                            git_messages.append("init failed")
                 else:
                     git_messages.append("git not available")
                 # Step 2: Install bundled git extension

From 7ab238c5d23bffd73c1e56cd35c5067f8d144750 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 16:03:44 -0500
Subject: [PATCH 11/13] fix: ensure_executable_scripts also covers
 .specify/extensions/ (#2117)

Extension .sh scripts (e.g. create-new-feature.sh, initialize-repo.sh)
may lack execute bits after install. Scan both .specify/scripts/ and
.specify/extensions/ for permission fixing.
---
 src/specify_cli/__init__.py | 64 ++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 30 deletions(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index e2d8926848..2440e55b7b 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -700,41 +700,45 @@ def _install_shared_infra(
 
 
 def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None = None) -> None:
-    """Ensure POSIX .sh scripts under .specify/scripts (recursively) have execute bits (no-op on Windows)."""
+    """Ensure POSIX .sh scripts under .specify/scripts and .specify/extensions (recursively) have execute bits (no-op on Windows)."""
     if os.name == "nt":
         return  # Windows: skip silently
-    scripts_root = project_path / ".specify" / "scripts"
-    if not scripts_root.is_dir():
-        return
+    scan_roots = [
+        project_path / ".specify" / "scripts",
+        project_path / ".specify" / "extensions",
+    ]
     failures: list[str] = []
     updated = 0
-    for script in scripts_root.rglob("*.sh"):
-        try:
-            if script.is_symlink() or not script.is_file():
-                continue
+    for scripts_root in scan_roots:
+        if not scripts_root.is_dir():
+            continue
+        for script in scripts_root.rglob("*.sh"):
             try:
-                with script.open("rb") as f:
-                    if f.read(2) != b"#!":
-                        continue
-            except Exception:
-                continue
-            st = script.stat()
-            mode = st.st_mode
-            if mode & 0o111:
-                continue
-            new_mode = mode
-            if mode & 0o400:
-                new_mode |= 0o100
-            if mode & 0o040:
-                new_mode |= 0o010
-            if mode & 0o004:
-                new_mode |= 0o001
-            if not (new_mode & 0o100):
-                new_mode |= 0o100
-            os.chmod(script, new_mode)
-            updated += 1
-        except Exception as e:
-            failures.append(f"{script.relative_to(scripts_root)}: {e}")
+                if script.is_symlink() or not script.is_file():
+                    continue
+                try:
+                    with script.open("rb") as f:
+                        if f.read(2) != b"#!":
+                            continue
+                except Exception:
+                    continue
+                st = script.stat()
+                mode = st.st_mode
+                if mode & 0o111:
+                    continue
+                new_mode = mode
+                if mode & 0o400:
+                    new_mode |= 0o100
+                if mode & 0o040:
+                    new_mode |= 0o010
+                if mode & 0o004:
+                    new_mode |= 0o001
+                if not (new_mode & 0o100):
+                    new_mode |= 0o100
+                os.chmod(script, new_mode)
+                updated += 1
+            except Exception as e:
+                failures.append(f"{script.relative_to(project_path)}: {e}")
     if tracker:
         detail = f"{updated} updated" + (f", {len(failures)} failed" if failures else "")
         tracker.add("chmod", "Set script permissions recursively")

From d81de9026e7954932ca42cc9cbf899ee011803cf Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 17:10:59 -0500
Subject: [PATCH 12/13] fix: move chmod after extension install + sanitize
 error_msg (#2117)

- ensure_executable_scripts() now runs after git extension install so
  extension .sh files get execute bits in the same init run
- Sanitize init_git_repo error_msg to single line (replace newlines,
  truncate to 120 chars) to prevent garbled StepTracker output
---
 src/specify_cli/__init__.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 2440e55b7b..56d84c0399 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1184,8 +1184,6 @@ def init(
             _install_shared_infra(project_path, selected_script, tracker=tracker)
             tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
 
-            ensure_executable_scripts(project_path, tracker=tracker)
-
             ensure_constitution_from_template(project_path, tracker=tracker)
 
             if not no_git:
@@ -1199,8 +1197,10 @@ def init(
                     if success:
                         git_messages.append("initialized")
                     else:
+                        # Sanitize multi-line error_msg to single line for tracker
                         if error_msg:
-                            git_messages.append(f"init failed: {error_msg}")
+                            sanitized = error_msg.replace('\n', ' ').strip()
+                            git_messages.append(f"init failed: {sanitized[:120]}")
                         else:
                             git_messages.append("init failed")
                 else:
@@ -1226,6 +1226,9 @@ def init(
             else:
                 tracker.skip("git", "--no-git flag")
 
+            # Fix permissions after all installs (scripts + extensions)
+            ensure_executable_scripts(project_path, tracker=tracker)
+
             # Persist the CLI options so later operations (e.g. preset add)
             # can adapt their behaviour without re-scanning the filesystem.
             # Must be saved BEFORE preset install so _get_skills_dir() works.

From 1416af067088256a563d558d7a7dd7242bf438ba Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Tue, 7 Apr 2026 17:49:11 -0500
Subject: [PATCH 13/13] fix: use tracker.error for git init/extension failures
 (#2117)

Git init failure and extension install failure were reported as
tracker.complete (showing green) even on error. Now track a
git_has_error flag and call tracker.error when any step fails,
so the UI correctly reflects the failure state.
---
 src/specify_cli/__init__.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 56d84c0399..ff049058e7 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1189,6 +1189,7 @@ def init(
             if not no_git:
                 tracker.start("git")
                 git_messages = []
+                git_has_error = False
                 # Step 1: Initialize git repo if needed
                 if is_git_repo(project_path):
                     git_messages.append("existing repo detected")
@@ -1197,6 +1198,7 @@ def init(
                     if success:
                         git_messages.append("initialized")
                     else:
+                        git_has_error = True
                         # Sanitize multi-line error_msg to single line for tracker
                         if error_msg:
                             sanitized = error_msg.replace('\n', ' ').strip()
@@ -1219,10 +1221,16 @@ def init(
                             )
                             git_messages.append("extension installed")
                     else:
+                        git_has_error = True
                         git_messages.append("bundled extension not found")
                 except Exception as ext_err:
+                    git_has_error = True
                     git_messages.append(f"extension install failed: {ext_err}")
-                tracker.complete("git", "; ".join(git_messages))
+                summary = "; ".join(git_messages)
+                if git_has_error:
+                    tracker.error("git", summary)
+                else:
+                    tracker.complete("git", summary)
             else:
                 tracker.skip("git", "--no-git flag")