docs: add workflows reference, reorganize into docs/reference/, and add --version flag (#2244)

* docs: add workflows reference, reorganize into docs/reference/, and add --version flag

- Move integrations.md, extensions.md, presets.md into docs/reference/
- New docs/reference/workflows.md: command reference for all workflow
  commands, built-in SDD Cycle workflow with Mermaid diagram, step types,
  expressions, input types, state/resume, and FAQ
- Rename workflow input feature_name to spec with prompt 'Describe what
  you want to build' to match speckit.specify command terminology
- Add --version / -V flag to root specify command with tests
- Update docs/toc.yml, README.md links, and docs/upgrade.md cross-reference
  to use reference/ paths
- Add workflow command to README CLI reference table

* docs: update speckit_version requirement to >=0.7.2 in workflow example

tests/test_cli_version.py

@@ -0,0 +1,35 @@
+"""Tests for the --version CLI flag."""
+
+from unittest.mock import patch
+
+from typer.testing import CliRunner
+
+from specify_cli import app
+
+
+runner = CliRunner()
+
+
+class TestVersionFlag:
+    """Test --version / -V flag on the root command."""
+
+    def test_version_long_flag(self):
+        """specify --version prints version and exits 0."""
+        with patch("specify_cli.get_speckit_version", return_value="1.2.3"):
+            result = runner.invoke(app, ["--version"])
+        assert result.exit_code == 0
+        assert "specify 1.2.3" in result.output
+
+    def test_version_short_flag(self):
+        """specify -V prints version and exits 0."""
+        with patch("specify_cli.get_speckit_version", return_value="1.2.3"):
+            result = runner.invoke(app, ["-V"])
+        assert result.exit_code == 0
+        assert "specify 1.2.3" in result.output
+
+    def test_version_flag_takes_precedence_over_subcommand(self):
+        """--version should work even when a subcommand follows."""
+        with patch("specify_cli.get_speckit_version", return_value="0.7.2"):
+            result = runner.invoke(app, ["--version", "init"])
+        assert result.exit_code == 0
+        assert "specify 0.7.2" in result.output