Basic operation of creating a new repo or enhancing an existing repo with git init.

.
├── branches
├── config
├── description
├── HEAD
├── hooks
│   ├── applypatch-msg.sample
│   ├── commit-msg.sample
│   ├── fsmonitor-watchman.sample
│   ├── post-update.sample
│   ├── pre-applypatch.sample
│   ├── pre-commit.sample
│   ├── prepare-commit-msg.sample
│   ├── pre-push.sample
│   ├── pre-rebase.sample
│   ├── pre-receive.sample
│   └── update.sample
├── info
│   └── exclude
├── objects
│   ├── info
│   └── pack
└── refs
    ├── heads
    └── tags

Running git init in an existing repository is safe. It will not
overwrite things that are already there. The primary reason for
rerunning git init is to pick up newly added templates (or to
move the repository to another place if --separate-git-dir is
given).

By default, git init will populate your new .git directory with the contents of /usr/share/git-core/templates/, without overwriting existing content of the same name:

├── branches
├── description
├── hooks
│   ├── applypatch-msg.sample
│   ├── commit-msg.sample
│   ├── fsmonitor-watchman.sample
│   ├── post-update.sample
│   ├── pre-applypatch.sample
│   ├── pre-commit.sample
│   ├── prepare-commit-msg.sample
│   ├── pre-push.sample
│   ├── pre-rebase.sample
│   ├── pre-receive.sample
│   └── update.sample
└── info
    └── exclude

You have the option of selecting a different template directory:

TEMPLATE DIRECTORY
       Files and directories in the template directory whose name do
       not start with a dot will be copied to the $GIT_DIR after it is
       created.

       The template directory will be one of the following (in order):

       ·   the argument given with the --template option;

       ·   the contents of the $GIT_TEMPLATE_DIR environment variable;

       ·   the init.templateDir configuration variable; or

       ·   the default template directory:
           /usr/share/git-core/templates.

       The default template directory includes some directory
       structure, suggested "exclude patterns" (see gitignore(5)), and
       sample hook files.

       The sample hooks are all disabled by default, To enable one of
       the sample hooks rename it by removing its .sample suffix.