fix(init): merge scaffold entries into an existing .gitignore instead of overwriting it

Re-running agentex init on an existing project replaced the user's
.gitignore. Keep the existing file and append only the scaffold entries that
are missing, with a test for the merge.

Claude-Session: https://claude.ai/code/session_01HCVKnA7LeJZ44nxZz1uzF3

Author: michaelxu2288

src/agentex/lib/cli/commands/init.py

@@ -119,7 +119,17 @@ def create_project_structure(
 
     for template, output in root_templates.items():
         output_path = project_dir / output
-        output_path.write_text(render_template(template, context, template_type))
+        rendered = render_template(template, context, template_type)
+        if output == ".gitignore" and output_path.exists():
+            # Re-running init on an existing project: keep the user's rules and
+            # append only the scaffold entries that are missing.
+            existing = output_path.read_text()
+            existing_lines = {line.strip() for line in existing.splitlines()}
+            missing = [line for line in rendered.splitlines() if line.strip() and not line.startswith("#") and line.strip() not in existing_lines]
+            if missing:
+                output_path.write_text(existing.rstrip("\n") + "\n\n# Added by agentex init\n" + "\n".join(missing) + "\n")
+            continue
+        output_path.write_text(rendered)
 
     console.print(f"\n[green]✓[/green] Created project structure at: {project_dir}")
 

tests/lib/cli/test_init_templates.py

@@ -148,3 +148,18 @@ def test_all_templates_ship_a_gitignore_that_excludes_env(tmp_path: Path, templa
     lines = gitignore.read_text().splitlines()
     assert ".env" in lines and ".venv/" in lines
     assert "!.env.example" in lines, "the example env file should stay committable"
+
+
+def test_rerunning_init_preserves_existing_gitignore_rules(tmp_path: Path):
+    """A pre-existing .gitignore keeps its own rules; missing scaffold entries are appended."""
+    context = _context(TemplateType.SYNC)
+    project_dir = tmp_path / context["project_name"]
+    project_dir.mkdir(parents=True)
+    (project_dir / ".gitignore").write_text("# mine\n*.log\n.env\n")
+
+    create_project_structure(tmp_path, context, TemplateType.SYNC, use_uv=True)
+
+    lines = (project_dir / ".gitignore").read_text().splitlines()
+    assert "*.log" in lines, "user rule was dropped"
+    assert lines.count(".env") == 1, "existing entry duplicated"
+    assert ".venv/" in lines and "!.env.example" in lines, "scaffold entries not appended"