Creating files again

please show the full source code, so it's clear _where_ this is invoked

Hello, Yann! This is a dialog:

public class StoryCreationDialog extends DialogWrapper

// the data is collected from the input fields

@NotNull
private JSONObject constructJsonObject() {
    final String title = titleField.getText();
    final int readingTime = Integer.parseInt(readingTimeField.getText());
    final String storyDescription = descriptionField.getText();
    final String language = languageField.getText();
    JSONObject storyJson = new JSONObject();
    storyJson.put("title", title);
    storyJson.put("readingTime", readingTime);
    storyJson.put("description", storyDescription);
    storyJson.put("program_lang", language);
    return storyJson;
}

// and then tries to save it upon submission

@Override
protected void doOKAction() {
    JSONObject storyJson = constructJsonObject();
    ApplicationManager.getApplication().runWriteAction((Runnable) () -> {
        File file = new File(".story.json");
        try (FileWriter writer = new FileWriter(file)) {
            final ObjectMapper objectMapper = new ObjectMapper();
            objectMapper.configure(SerializationFeature.INDENT_OUTPUT, true);
            final JsonNode tree = objectMapper.readTree(storyJson.toJSONString());
            writer.write(objectMapper.writeValueAsString(tree));
            writer.flush();
            final VirtualFile newParent = VfsUtil.createDirectories(file.getParent());
            if (newParent != null) {
                final VirtualFile virtualFile = LocalFileSystem.getInstance().refreshAndFindFileByIoFile(file);
                VfsUtilCore.copyFile(this, virtualFile, newParent);
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    });
    dispose();
}

What is

File file = new File(".story.json")

exactly? You're not specifying the parent directory where the file is created, but try to access file.getParent() later