diff --git a/src/gitingest/ingest_from_query.py b/src/gitingest/ingest_from_query.py
index 0852c227..902ad89c 100644
--- a/src/gitingest/ingest_from_query.py
+++ b/src/gitingest/ingest_from_query.py
@@ -151,7 +151,13 @@ def _read_file_content(file_path: str) -> str:
 
 def _sort_children(children: list[dict[str, Any]]) -> list[dict[str, Any]]:
     """
-    Sort children nodes with files first, then directories, both in alphanumerical order.
+    Sort children nodes with:
+    1. README.md first
+    2. Regular files (not starting with dot)
+    3. Hidden files (starting with dot)
+    4. Regular directories (not starting with dot)
+    5. Hidden directories (starting with dot)
+    All groups are sorted alphanumerically within themselves.
 
     Parameters
     ----------
@@ -161,11 +167,30 @@ def _sort_children(children: list[dict[str, Any]]) -> list[dict[str, Any]]:
     Returns
     -------
     list[dict[str, Any]]
-        Sorted list with files first, followed by directories.
+        Sorted list according to the specified order.
     """
-    files = sorted([child for child in children if child["type"] == "file"], key=lambda x: x["name"])
-    directories = sorted([child for child in children if child["type"] == "directory"], key=lambda x: x["name"])
-    return files + directories
+    # Separate files and directories
+    files = [child for child in children if child["type"] == "file"]
+    directories = [child for child in children if child["type"] == "directory"]
+
+    # Find README.md
+    readme_files = [f for f in files if f["name"].lower() == "readme.md"]
+    other_files = [f for f in files if f["name"].lower() != "readme.md"]
+
+    # Separate hidden and regular files/directories
+    regular_files = [f for f in other_files if not f["name"].startswith(".")]
+    hidden_files = [f for f in other_files if f["name"].startswith(".")]
+    regular_dirs = [d for d in directories if not d["name"].startswith(".")]
+    hidden_dirs = [d for d in directories if d["name"].startswith(".")]
+
+    # Sort each group alphanumerically
+    regular_files.sort(key=lambda x: x["name"])
+    hidden_files.sort(key=lambda x: x["name"])
+    regular_dirs.sort(key=lambda x: x["name"])
+    hidden_dirs.sort(key=lambda x: x["name"])
+
+    # Combine all groups in the desired order
+    return readme_files + regular_files + hidden_files + regular_dirs + hidden_dirs
 
 
 def _scan_directory(
@@ -412,7 +437,7 @@ def _create_file_content_string(files: list[dict[str, Any]]) -> str:
     Create a formatted string of file contents with separators.
 
     This function takes a list of files and generates a formatted string where each file’s
-    content is separated by a divider. If a README.md file is found, it is placed at the top.
+    content is separated by a divider.
 
     Parameters
     ----------
@@ -427,21 +452,9 @@ def _create_file_content_string(files: list[dict[str, Any]]) -> str:
     output = ""
     separator = "=" * 48 + "\n"
 
-    # First add README.md if it exists
-    for file in files:
-        if not file["content"]:
-            continue
-
-        if file["path"].lower() == "/readme.md":
-            output += separator
-            output += f"File: {file['path']}\n"
-            output += separator
-            output += f"{file['content']}\n\n"
-            break
-
     # Then add all other files in their original order
     for file in files:
-        if not file["content"] or file["path"].lower() == "/readme.md":
+        if not file["content"]:
             continue
 
         output += separator