fix: implicitly add --force when only engine-owned dirs exist

When the workflow engine creates .specify/workflows/runs/ before steps
execute, the directory is technically non-empty. Previously, specify init
would prompt for confirmation (hanging in unattended mode) unless the
user explicitly set force: true. Now the step detects that only
engine-owned directories (.specify/) are present and implicitly adds
--force so init proceeds without user interaction.

Also fixes the test to exercise the implicit-force path rather than
passing force: True explicitly (which bypassed the check entirely).

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

Author: mnriem

src/specify_cli/workflows/steps/init/__init__.py

@@ -107,18 +107,21 @@ def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
         # ``specify init`` prompts for confirmation if the directory is not
         # empty.  Workflows run unattended (no stdin), so the prompt would
         # abort with a confusing error.  Fail fast with an actionable message.
+        # Exception: if the only pre-existing content is engine-owned (e.g.
+        # .specify/workflows/runs/), treat it as implicitly empty and auto-add
+        # --force so init can proceed unattended.
         targets_current_dir = here or not project or str(project) == "."
         if targets_current_dir and not force:
             base = context.project_root or os.getcwd()
             try:
                 with os.scandir(base) as it:
-                    not_empty = any(
+                    non_engine_entries = [
                         entry for entry in it
                         if entry.name not in _ENGINE_OWNED_DIRS
-                    )
+                    ]
             except OSError:
-                not_empty = False
-            if not_empty:
+                non_engine_entries = []
+            if non_engine_entries:
                 error_message = (
                     f"Target directory {base!r} is not empty. Set "
                     "'force: true' to merge into a non-empty directory."
@@ -138,6 +141,10 @@ def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
                     },
                     error=error_message,
                 )
+            else:
+                # Only engine-owned dirs exist — implicitly force so specify
+                # init doesn't prompt about the non-empty directory.
+                force = True
 
         if integration:
             argv.extend(["--integration", str(integration)])

tests/test_workflows.py

@@ -1086,10 +1086,12 @@ def test_engine_owned_dirs_do_not_trigger_non_empty_check(self, tmp_path):
             project_root=str(tmp_path), default_integration="copilot"
         )
         result = step.execute(
-            {"id": "bootstrap", "here": True, "script": "sh", "force": True},
+            {"id": "bootstrap", "here": True, "script": "sh"},
             ctx,
         )
         assert result.status == StepStatus.COMPLETED
+        # Verify --force was implicitly added
+        assert "--force" in result.output["argv"]
 
     def test_default_integration_when_none_provided(self, tmp_path):
         from specify_cli.workflows.steps.init import InitStep