Some projects (the Git project itself for example) store additional files directly in the Git file system without them necessarily being a checked in file.
Let’s start off by storing a random file in Git:
$ echo "Foo" | git hash-object -w --stdin
51fc03a9bb365fae74fd2bf66517b30bf48020cb
At this point the object is in the database, but if you don’t set something up to point to that object it will be garbage collected. The easiest way is to tag it: