This is fixed in update-manager 1:18.04.4.

** Description changed:

+ [Impact]
+ 
  Empty directories can't be stored in Git, which is a very popular
  version control system for maintaining source packages.
  
  Keeping the empty directory in the source package prevent others from
  easily contributing to the package by importing it in full to a local
  repository, making changes, then generating an updated source package
  with tools like git-buildpackage. In that workflow the empty directory
  would be lost potentially causing errors if the installed binary package
  relied on it or causing autopkgtest failures if tests used it.
+ 
+ The backport to a stable release helps further maintenance of the
+ package in git-based workflows and avoids accidentally breaking
+ autopkgtests when the existence of the empty dirs matter.
+ 
+ The upload may drop the empty dirs or place placeholder (e.g.: */.keep)
+ files  in the source package.
+ 
+ [Test Case]
+ 
+ Extract the source package, then run the following command int the
+ extracted source directory:
+ 
+  find . -depth -type d -empty
+ 
+ [Regression Potential]
+ 
+ The removed directories or the added placeholders may cause run-time
+ issues or cause autopkgtest failures. To prevent those please check that
+ the placeholder files are not shipped in the binary packages and also
+ run autokgtests.

** Changed in: update-manager (Ubuntu)
       Status: New => Fix Released

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https://bugs.launchpad.net/bugs/1758963

Title:
  Please don't ship empty directories in the source package

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