Enhancement: Include empty and unlisted folders in the generated output file

[moisesuailab]

Currently, when using the command npx codemerge init to create the configuration file, and then running npx codemerge use to generate the merged file, I noticed that empty folders and those containing unlisted files (such as PNG files) are not included in the generated output.

This affects the visibility of the complete project structure, especially when there are empty folders or files that are not specified in the configuration but are still important for the project’s organization.

Suggested improvement:

It would be helpful if the complete folder structure was preserved in the output file (except for folders explicitly excluded in the configuration file), even if those folders are empty or contain unlisted files. At the very least, the directory tree structure should be preserved, even if files are not included.

Steps to reproduce:

1. Run the command npx codemerge init to create the configuration file.

2. Run the command npx codemerge use to generate the merged file.

3. Observe that empty folders or folders with unlisted files are not included in the generated output file.

Expected behavior:

The generated file should include the complete folder structure, excluding those explicitly mentioned in the configuration file. Empty folders or those with unlisted files should be retained in the output structure, at least as a directory tree representation.