In my pkgmeta for TellMeWhen, I had /Lib listed as an ignore.
With the old packager, this would cause the /Lib folder to get wiped prior to being re-populated by my externals, ensuring that the packaged libs were always exactly as they come in from the externals, with no extra files hanging around.
In the new packager, this causes my /Lib folder to be excluded entirely from the resulting zip. It (presumably) gets populated with externals, but then never gets included when the zip is created.
Some documentation about the order in which pkgmeta directives are processed would be appreciated.
The behavioral change was made to accommodate a longstanding request to have the ignore directive actually work on externals that are pulled in. For example, anyone that uses the pkgmeta to pull down LibStub will have a /tests folder inside of that. Previously, the ignore directive would not work on that folder. The new behavior is to pull everything down, then process the ignore directive, ensuring everything that is listed will, in fact, be ignored.
EDIT: All VCS systems we support have a built-in mechanism for ignoring things so they aren't added to the actual repository.