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When you deploy a phase to the next, all files that correspond to the standard folders of a Joomla! installation are synced and kept equal. That means that any files that were not in the original phase will be deleted. That also means that any other folders that are in your docroot and don't belong to the CMS standard folders are not synced.

Excluding files or folders from being syncronized

If you need to exclude some files or folders from being syncronized, you just need to create a file in the develop phase using the Code Editor. The file has to be named

.files_exclude

And there you have to include a list of files or folders you do not want to syncronize.
E.g. you have a folder inside the /images folder named "customer" and you do not want to include that folder in the workflow.
You just have to include it in the .files_exclude file like this:

images/customer                                                                                                                                                                               

Including other files or folders in the syncronization

On the other hand, if you need to include some other folders in the workflow, e.g. a "downloads" or "pdfs" folder that you need to have consistent throughout the development cycle, you have to create a file in the Develop phase using the Code Editor. The file has to be named

.files_include

Inside that file you have to add the list of files or folders that you want to include in the workflow, e.g. "downloads"

downloads
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