This is common amongst ruby projects in eclipse.

Unless full paths are used .gitignore, all matching files and folders will be ignored, however deep they are in the repo.

For example, ignoring log/* doesn't just ignore all log files, but also files such as lib/project/log/awesome_logger.rb.  It's a mistake I've made a couple of times but never seemed to have learned from.

(https://github.com/lsegal/yard)

Should be in Global/TextMate.gitignore