feat: make git extension opt-in and remove --no-git at v0.10.0 (#2873)

* feat(init)!: make git extension opt-in and remove --no-git at v0.10.0

- Remove --no-git parameter from specify init command
- Remove git extension auto-installation from init flow
- Git repository initialization (git init) still runs when git is available
- Remove --no-git from all test invocations across the test suite
- Update docs to reflect opt-in git extension behavior
- Replace TestGitExtensionAutoInstall with TestGitExtensionOptIn tests

BREAKING CHANGE: specify init no longer auto-installs the git extension.
Use `specify extension add git` to install it explicitly.
The --no-git flag has been removed.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* refactor(scripts): remove git operations from core scripts

Git functionality is now entirely managed by the git extension.
Core scripts only handle directory-based feature creation and numbering.

- Remove has_git(), check_feature_branch(), git branch creation from core
- Simplify number detection to use only spec directory scanning
- Remove HAS_GIT output from get_feature_paths()
- Remove git remote fetching and branch querying
- Keep BRANCH_NAME output key for backward compatibility

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* refactor: remove all git operations from core

- Remove is_git_repo() and init_git_repo() dead code from _utils.py
- Remove --branch-numbering from init command
- Remove git from 'specify check' (now extension-only)
- Update docs: git is optional prerequisite, check command description
- Fix tests to reflect no-git-in-core reality (fallback to main)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* refactor(scripts): remove directory scanning and branch fallback from core

Core scripts now resolve feature context exclusively from:
1. SPECIFY_FEATURE env var (set by git extension)
2. .specify/feature.json (persisted by specify command)

Removed find_feature_dir_by_prefix() and directory scanning heuristics —
these are the git extension's responsibility. Scripts error clearly when
no feature context is available.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* feat: introduce feature_numbering, deprecate branch_numbering in init-options

- specify command template now reads feature_numbering (preferred) with
  fallback to branch_numbering (deprecated) from init-options.json
- Git extension reads git-config.yml > feature_numbering > branch_numbering
- init now writes feature_numbering: sequential to init-options.json
- Deprecation warning emitted when branch_numbering is used as fallback

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: remove trailing whitespace in common.ps1

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* feat(scripts): persist SPECIFY_FEATURE_DIRECTORY env var to feature.json

When SPECIFY_FEATURE_DIRECTORY is set, get_feature_paths() now writes the
value to .specify/feature.json so future sessions without the env var can
still resolve the feature directory. The write is idempotent — it skips
when the file already contains the same value.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address review feedback — error messages and docs

- Update error messages in common.sh and common.ps1 to reference
  SPECIFY_FEATURE_DIRECTORY instead of SPECIFY_FEATURE (which no longer
  resolves feature directories)
- Fix get_current_branch comment (returns empty string, not error)
- Update upgrade.md to reference SPECIFY_FEATURE_DIRECTORY with correct
  example paths
- Update local-development.md troubleshooting: replace stale 'Git step
  skipped' row with actionable git extension guidance

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(scripts): harden feature.json persistence

- Use json_escape in printf fallback when jq is unavailable (common.sh)
- Replace utf8NoBOM encoding with UTF8Encoding($false) for PowerShell
  5.1 compatibility (common.ps1)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* refactor(scripts): remove dead feature_json_matches_feature_dir functions

These guards are no longer needed since the branch-name validation they
protected against has been removed from check-prerequisites.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* refactor(git-ext): rename create-new-feature to create-new-feature-branch

The git extension's script only creates the git branch — rename it to
reflect that responsibility. The core create-new-feature.sh/.ps1 handles
feature directory creation and feature.json persistence.

Also includes fixes from review feedback:
- common.sh: _persist_feature_json uses json_escape fallback
- common.ps1: Save-FeatureJson uses UTF8Encoding for PS 5.1 compat
- common.ps1: case-sensitive path stripping on non-Windows
- create-new-feature.sh/ps1: output both SPECIFY_FEATURE and
  SPECIFY_FEATURE_DIRECTORY
- setup-tasks.sh: fix stale 'Validate branch' comment

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(tests): update references to renamed git extension scripts

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(tests): remove duplicate EXT_CREATE_FEATURE assignments

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Manfred Riem <mnriem@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/specify_cli/_utils.py

@@ -77,51 +77,6 @@ def check_tool(tool: str, tracker=None) -> bool:
     return found
 
 
-def is_git_repo(path: Path | None = 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, str | None]:
-    """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.