fix nested code blocks in file content making filenames of commands

aider/coders/wholefile_coder.py

@@ -33,9 +33,23 @@ def get_edits(self, mode="update"):
         fname = None
         fname_source = None
         new_lines = []
+        inner_fence_depth = 0
         for i, line in enumerate(lines):
             if line.startswith(self.fence[0]) or line.startswith(self.fence[1]):
                 if fname is not None:
+                    # Check if this fence is nested inside the file block
+                    stripped = line.strip()
+                    if stripped != self.fence[0] and stripped != self.fence[1]:
+                        # Has a language specifier — opening inner fence, treat as content
+                        inner_fence_depth += 1
+                        new_lines.append(line)
+                        continue
+                    elif inner_fence_depth > 0:
+                        # Plain fence closing an inner fence
+                        inner_fence_depth -= 1
+                        new_lines.append(line)
+                        continue
+
                     # ending an existing block
                     saw_fname = None
 
@@ -49,9 +63,11 @@ def get_edits(self, mode="update"):
                     fname = None
                     fname_source = None
                     new_lines = []
+                    inner_fence_depth = 0
                     continue
 
                 # fname==None ... starting a new block
+                inner_fence_depth = 0
                 if i > 0:
                     fname_source = "block"
                     fname = lines[i - 1].strip()

tests/basic/test_wholefile.py

@@ -316,6 +316,34 @@ def test_update_named_file_but_extra_unnamed_code_block(self):
             updated_content = f.read()
         self.assertEqual(updated_content, new_content)
 
+    def test_nested_code_blocks_in_file_content(self):
+        # Issue #4225: README.md with inner ```bash blocks caused inner fence lines
+        # to be treated as file block boundaries, splitting content incorrectly.
+        sample_file = "README.md"
+
+        io = InputOutput(yes=True)
+        coder = WholeFileCoder(main_model=self.GPT35, io=io, fnames=[sample_file])
+
+        expected_content = (
+            "# My Project\n\n"
+            "## Installation\n\n"
+            "```bash\n"
+            "git clone <this-repo>\n"
+            "npm install\n"
+            "```\n\n"
+            "## Usage\n\n"
+            "```bash\n"
+            "npm run dev\n"
+            "```\n"
+        )
+
+        coder.partial_response_content = f"{sample_file}\n```\n{expected_content}```"
+
+        edited_files = coder.apply_updates()
+
+        self.assertIn(sample_file, edited_files)
+        self.assertEqual(Path(sample_file).read_text(), expected_content)
+
     def test_full_edit(self):
         # Create a few temporary files
         _, file1 = tempfile.mkstemp()