Don't add unnecessary [tool] section to pyproject.toml when running pyrefly init

Summary: Fixes #1948.

Reviewed By: kinto0

Differential Revision: D89901293

fbshipit-source-id: c2a62c7ddabbe356cd1c02dbd89569cdcce0508d

Author: rchen152

crates/pyrefly_config/src/pyproject.rs

@@ -59,10 +59,14 @@ impl PyProject {
             if let Some(tool_table) = config_doc.get("tool")
                 && let Some(pyrefly_table) = tool_table.get("pyrefly")
             {
+                let is_new_tool_table = !doc.contains_key("tool");
                 let tool_entry = doc
                     .entry("tool")
                     .or_insert(toml_edit::Item::Table(toml_edit::Table::new()));
                 if let Some(tool_table_mut) = tool_entry.as_table_mut() {
+                    if is_new_tool_table {
+                        tool_table_mut.set_implicit(true);
+                    }
                     tool_table_mut.remove("pyrefly");
                     let max_tool_pos = tool_table_mut
                         .iter()
@@ -137,6 +141,31 @@ line-length = 88
         Ok(())
     }
 
+    #[test]
+    fn test_add_pyrefly_config_to_existing_pyproject() -> anyhow::Result<()> {
+        let tmp = tempfile::tempdir()?;
+        let pyproject_path = tmp.path().join("pyproject.toml");
+
+        let existing_content = "\n";
+        fs_anyhow::write(&pyproject_path, existing_content)?;
+
+        let config = ConfigFile {
+            project_includes: Globs::new(vec!["new/path/**/*.py".to_owned()]).unwrap(),
+            ..Default::default()
+        };
+        PyProject::update(&pyproject_path, config)?;
+
+        let updated_content = fs_anyhow::read_to_string(&pyproject_path)?;
+
+        assert!(updated_content.contains("[tool.pyrefly]"));
+        assert!(updated_content.contains("project-includes = [\"new/path/**/*.py\"]"));
+
+        // Regression test for bug where we would insert an unnecessary [tool] section
+        assert!(!updated_content.contains("[tool]"));
+
+        Ok(())
+    }
+
     #[test]
     fn test_pyrefly_section_ordering() -> anyhow::Result<()> {
         let tmp = tempfile::tempdir()?;