Или, по крайней мере, одна метамодель JPA должна присутствовать !, или почему я получаю неправильную фабрику фасоли?

Еще один пример перехода по структуре каталогов, чтобы получить именно то, что вы хотите. Примечание: я не исключил Library/, но Library/**/*

# .gitignore file
Library/**/*
!Library/Application Support/
!Library/Application Support/Sublime Text 3/
!Library/Application Support/Sublime Text 3/Packages/
!Library/Application Support/Sublime Text 3/Packages/User/
!Library/Application Support/Sublime Text 3/Packages/User/*macro
!Library/Application Support/Sublime Text 3/Packages/User/*snippet
!Library/Application Support/Sublime Text 3/Packages/User/*settings
!Library/Application Support/Sublime Text 3/Packages/User/*keymap
!Library/Application Support/Sublime Text 3/Packages/User/*theme
!Library/Application Support/Sublime Text 3/Packages/User/**/
!Library/Application Support/Sublime Text 3/Packages/User/**/*macro
!Library/Application Support/Sublime Text 3/Packages/User/**/*snippet
!Library/Application Support/Sublime Text 3/Packages/User/**/*settings
!Library/Application Support/Sublime Text 3/Packages/User/**/*keymap
!Library/Application Support/Sublime Text 3/Packages/User/**/*theme

> git add Library

> git status

On branch master
Your branch is up-to-date with 'origin/master'.
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    new file:   Library/Application Support/Sublime Text 3/Packages/User/Default (OSX).sublime-keymap
    new file:   Library/Application Support/Sublime Text 3/Packages/User/ElixirSublime.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/Package Control.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/RESTer.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/SublimeLinter/Monokai (SL).tmTheme
    new file:   Library/Application Support/Sublime Text 3/Packages/User/TextPastryHistory.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/ZenTabs.sublime-settings
    new file:   Library/Application Support/Sublime Text 3/Packages/User/adrian-comment.sublime-macro
    new file:   Library/Application Support/Sublime Text 3/Packages/User/json-pretty-generate.sublime-snippet
    new file:   Library/Application Support/Sublime Text 3/Packages/User/raise-exception.sublime-snippet
    new file:   Library/Application Support/Sublime Text 3/Packages/User/trailing_spaces.sublime-settings