fix: preserve feature numbering during reinitialization

src/specify_cli/command_init.py

@@ -853,7 +853,7 @@ def init(
                     "integration": resolved_integration.key,
                     "here": here,
                     "script": selected_script,
-                    "feature_numbering": "sequential",
+                    "feature_numbering": previous_init_options.get("feature_numbering", "sequential"),
                     "speckit_version": get_speckit_version(),
                     "allow_symlinks": allow_symlinks,
                 }

tests/specify_cli/test_command_init.py

@@ -17,6 +17,7 @@
 from __future__ import annotations
 
 import importlib
+import json
 import os
 import re
 import subprocess
@@ -93,6 +94,34 @@ def _init(tmp_path: Path, name: str):
         os.chdir(previous)
 
 
+@pytest.mark.parametrize("numbering", ["timestamp", "sequential", None])
+def test_reinit_preserves_feature_numbering(tmp_path: Path, monkeypatch, numbering):
+    result = _init(tmp_path, "proj")
+    assert result.exit_code == 0, _strip(result.stdout)
+    project = tmp_path / "proj"
+    options_path = project / ".specify" / "init-options.json"
+    options = json.loads(options_path.read_text(encoding="utf-8"))
+    assert options["feature_numbering"] == "sequential"
+    if numbering is None:
+        options.pop("feature_numbering")
+    else:
+        options["feature_numbering"] = numbering
+    options["custom_setting"] = "keep me"
+    options_path.write_text(json.dumps(options), encoding="utf-8")
+
+    monkeypatch.chdir(project)
+    result = CliRunner().invoke(app, [
+        "init", "--here", "--force", "--integration", "generic",
+        "--integration-options", "--commands-dir .agent/commands",
+        "--script", "sh", "--non-interactive", "--ignore-agent-tools", "--offline",
+    ])
+    assert result.exit_code == 0, _strip(result.stdout)
+    updated = json.loads(options_path.read_text(encoding="utf-8"))
+    assert updated["feature_numbering"] == (numbering or "sequential")
+    assert updated["custom_setting"] == "keep me"
+    assert updated["here"] is True
+
+
 @pytest.mark.parametrize("name", ["proj [v2]", "my[bold]app"])
 def test_next_steps_cd_shows_the_real_project_name(tmp_path: Path, name: str):
     """The `cd` line must name the directory that was actually created."""